{ "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": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "assays": [ { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0011028", "name": "olfactory ensheathing cell" }, "cellTypeAuthorAnnotation": "OEC1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.284720, "sdRefIntergenicDistribution": 2.295629, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 527817, "distinctRankCount": 1207, "maxRank": 24740.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0011028", "name": "olfactory ensheathing cell" }, "cellTypeAuthorAnnotation": "OEC2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.023852, "sdRefIntergenicDistribution": 2.347347, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 596338, "distinctRankCount": 1256, "maxRank": 24759.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0011028", "name": "olfactory ensheathing cell" }, "cellTypeAuthorAnnotation": "OEC3", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.677016, "sdRefIntergenicDistribution": 2.222362, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 606402, "distinctRankCount": 883, "maxRank": 24814.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0011028", "name": "olfactory ensheathing cell" }, "cellTypeAuthorAnnotation": "OEC4", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.711156, "sdRefIntergenicDistribution": 2.647324, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1313204, "distinctRankCount": 1706, "maxRank": 25457.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0011028", "name": "olfactory ensheathing cell" }, "cellTypeAuthorAnnotation": "OEC5", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.598609, "sdRefIntergenicDistribution": 2.123196, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 333532, "distinctRankCount": 890, "maxRank": 24172.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000129", "name": "microglial cell" }, "cellTypeAuthorAnnotation": "MicroG1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.601688, "sdRefIntergenicDistribution": 2.158604, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 231039, "distinctRankCount": 731, "maxRank": 23755.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000129", "name": "microglial cell" }, "cellTypeAuthorAnnotation": "MicroG2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.303825, "sdRefIntergenicDistribution": 2.624767, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 935968, "distinctRankCount": 1482, "maxRank": 25276.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000129", "name": "microglial cell" }, "cellTypeAuthorAnnotation": "MicroG3", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.872970, "sdRefIntergenicDistribution": 1.957753, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 196522, "distinctRankCount": 454, "maxRank": 23493.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.386918, "sdRefIntergenicDistribution": 2.665830, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 943640, "distinctRankCount": 1614, "maxRank": 25372.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N10", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.421579, "sdRefIntergenicDistribution": 2.658971, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 924905, "distinctRankCount": 1843, "maxRank": 25339.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N11", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.546930, "sdRefIntergenicDistribution": 2.912818, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 687271, "distinctRankCount": 3007, "maxRank": 25811.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N12", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.273290, "sdRefIntergenicDistribution": 2.094094, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 227275, "distinctRankCount": 847, "maxRank": 24200.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N13", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.648197, "sdRefIntergenicDistribution": 2.541722, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 777143, "distinctRankCount": 1516, "maxRank": 25255.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N14", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.292354, "sdRefIntergenicDistribution": 2.112900, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 163281, "distinctRankCount": 1009, "maxRank": 23985.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N15", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.434360, "sdRefIntergenicDistribution": 1.969507, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 128532, "distinctRankCount": 353, "maxRank": 23068.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N16", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.221179, "sdRefIntergenicDistribution": 1.951871, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 164236, "distinctRankCount": 862, "maxRank": 23565.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 31.683427, "sdRefIntergenicDistribution": 1.679539, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 35882, "distinctRankCount": 374, "maxRank": 21449.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N3", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.124689, "sdRefIntergenicDistribution": 1.830518, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 96125, "distinctRankCount": 400, "maxRank": 22601.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N4", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 20.333774, "sdRefIntergenicDistribution": 1.806216, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 57187, "distinctRankCount": 492, "maxRank": 22231.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N5", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.708863, "sdRefIntergenicDistribution": 2.092417, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 184565, "distinctRankCount": 319, "maxRank": 22638.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N6", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.124734, "sdRefIntergenicDistribution": 2.490455, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 799249, "distinctRankCount": 795, "maxRank": 25046.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N7", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.950603, "sdRefIntergenicDistribution": 2.034317, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 154102, "distinctRankCount": 333, "maxRank": 23144.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N8", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.042748, "sdRefIntergenicDistribution": 2.914163, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 778743, "distinctRankCount": 1535, "maxRank": 25438.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N9", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.661532, "sdRefIntergenicDistribution": 2.736436, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 554272, "distinctRankCount": 1318, "maxRank": 25348.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0008019", "name": "mesenchymal cell" }, "cellTypeAuthorAnnotation": "Mes1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.169919, "sdRefIntergenicDistribution": 1.968485, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 271003, "distinctRankCount": 767, "maxRank": 24177.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0008019", "name": "mesenchymal cell" }, "cellTypeAuthorAnnotation": "Mes2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.679870, "sdRefIntergenicDistribution": 1.825524, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 149619, "distinctRankCount": 698, "maxRank": 23440.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000127", "name": "astrocyte" }, "cellTypeAuthorAnnotation": "Astro1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.128110, "sdRefIntergenicDistribution": 2.665228, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1027785, "distinctRankCount": 1592, "maxRank": 25449.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000127", "name": "astrocyte" }, "cellTypeAuthorAnnotation": "Astro2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 18.717712, "sdRefIntergenicDistribution": 1.750380, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 64061, "distinctRankCount": 359, "maxRank": 22260.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000127", "name": "astrocyte" }, "cellTypeAuthorAnnotation": "Astro3", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.929994, "sdRefIntergenicDistribution": 2.141075, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 373937, "distinctRankCount": 594, "maxRank": 24395.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000071", "name": "blood vessel endothelial cell" }, "cellTypeAuthorAnnotation": "EC1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.184797, "sdRefIntergenicDistribution": 2.377663, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 864072, "distinctRankCount": 1466, "maxRank": 25147.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000071", "name": "blood vessel endothelial cell" }, "cellTypeAuthorAnnotation": "EC2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.456464, "sdRefIntergenicDistribution": 1.966010, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 208836, "distinctRankCount": 593, "maxRank": 23988.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Mφ", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.694181, "sdRefIntergenicDistribution": 1.876955, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 151790, "distinctRankCount": 619, "maxRank": 23488.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0002453", "name": "oligodendrocyte precursor cell" }, "cellTypeAuthorAnnotation": "OPC", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.495031, "sdRefIntergenicDistribution": 2.029314, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 221023, "distinctRankCount": 1022, "maxRank": 24119.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000576", "name": "monocyte" }, "cellTypeAuthorAnnotation": "Mono", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.252370, "sdRefIntergenicDistribution": 1.850687, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 159832, "distinctRankCount": 628, "maxRank": 23430.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0008034", "name": "mural cell" }, "cellTypeAuthorAnnotation": "Mural1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.659822, "sdRefIntergenicDistribution": 1.819804, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 131923, "distinctRankCount": 689, "maxRank": 23434.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0008034", "name": "mural cell" }, "cellTypeAuthorAnnotation": "Mural2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.749522, "sdRefIntergenicDistribution": 1.935130, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 172699, "distinctRankCount": 585, "maxRank": 23860.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000232", "name": "erythrocyte" }, "cellTypeAuthorAnnotation": "RBCs", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 17.327213, "sdRefIntergenicDistribution": 1.704746, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 70383, "distinctRankCount": 102, "maxRank": 20083.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 567078668, "mappedReadsCount": 360557702, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947724" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000128", "name": "oligodendrocyte" }, "cellTypeAuthorAnnotation": "MyOligo", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.321966, "sdRefIntergenicDistribution": 2.141132, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 359070, "distinctRankCount": 1115, "maxRank": 24028.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0011028", "name": "olfactory ensheathing cell" }, "cellTypeAuthorAnnotation": "OEC1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.901783, "sdRefIntergenicDistribution": 2.398112, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 653103, "distinctRankCount": 1399, "maxRank": 24941.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0011028", "name": "olfactory ensheathing cell" }, "cellTypeAuthorAnnotation": "OEC2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.157001, "sdRefIntergenicDistribution": 2.345751, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 573799, "distinctRankCount": 1317, "maxRank": 24795.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0011028", "name": "olfactory ensheathing cell" }, "cellTypeAuthorAnnotation": "OEC3", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.698047, "sdRefIntergenicDistribution": 2.027044, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 392894, "distinctRankCount": 682, "maxRank": 24395.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0011028", "name": "olfactory ensheathing cell" }, "cellTypeAuthorAnnotation": "OEC4", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.918964, "sdRefIntergenicDistribution": 2.577600, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1141148, "distinctRankCount": 1714, "maxRank": 25364.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0011028", "name": "olfactory ensheathing cell" }, "cellTypeAuthorAnnotation": "OEC5", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.946385, "sdRefIntergenicDistribution": 2.062150, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 300926, "distinctRankCount": 944, "maxRank": 24101.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000129", "name": "microglial cell" }, "cellTypeAuthorAnnotation": "MicroG1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.452450, "sdRefIntergenicDistribution": 2.258921, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 372730, "distinctRankCount": 1038, "maxRank": 24148.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000129", "name": "microglial cell" }, "cellTypeAuthorAnnotation": "MicroG2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.853865, "sdRefIntergenicDistribution": 2.497850, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 690759, "distinctRankCount": 1338, "maxRank": 24931.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000129", "name": "microglial cell" }, "cellTypeAuthorAnnotation": "MicroG3", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.705916, "sdRefIntergenicDistribution": 1.831201, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 110161, "distinctRankCount": 325, "maxRank": 22571.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.382094, "sdRefIntergenicDistribution": 2.661497, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 982670, "distinctRankCount": 1818, "maxRank": 25438.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N10", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.189070, "sdRefIntergenicDistribution": 2.517331, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 630807, "distinctRankCount": 1649, "maxRank": 25048.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N11", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.774864, "sdRefIntergenicDistribution": 2.972607, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 671869, "distinctRankCount": 3100, "maxRank": 25896.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N12", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.083362, "sdRefIntergenicDistribution": 2.046821, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 198690, "distinctRankCount": 820, "maxRank": 24014.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N13", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.529973, "sdRefIntergenicDistribution": 2.343928, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 513787, "distinctRankCount": 1307, "maxRank": 24816.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N14", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.484244, "sdRefIntergenicDistribution": 1.976534, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 106982, "distinctRankCount": 859, "maxRank": 23494.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N15", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.876244, "sdRefIntergenicDistribution": 1.817829, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 90629, "distinctRankCount": 338, "maxRank": 22690.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N16", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.524899, "sdRefIntergenicDistribution": 1.786636, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 91464, "distinctRankCount": 636, "maxRank": 22874.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 52.156732, "sdRefIntergenicDistribution": 1.570498, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20560, "distinctRankCount": 245, "maxRank": 20752.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N3", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 15.777215, "sdRefIntergenicDistribution": 1.741614, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 79066, "distinctRankCount": 432, "maxRank": 22234.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N4", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.814073, "sdRefIntergenicDistribution": 1.879355, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 88470, "distinctRankCount": 710, "maxRank": 22879.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N5", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.562901, "sdRefIntergenicDistribution": 1.995807, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 128305, "distinctRankCount": 276, "maxRank": 21819.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N6", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.011702, "sdRefIntergenicDistribution": 2.051099, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 137643, "distinctRankCount": 317, "maxRank": 23041.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N7", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 20.322957, "sdRefIntergenicDistribution": 1.818380, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 60945, "distinctRankCount": 209, "maxRank": 21853.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N8", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.665274, "sdRefIntergenicDistribution": 2.795550, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 591057, "distinctRankCount": 1388, "maxRank": 25254.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N9", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.852899, "sdRefIntergenicDistribution": 2.556553, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 359794, "distinctRankCount": 1085, "maxRank": 25110.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0008019", "name": "mesenchymal cell" }, "cellTypeAuthorAnnotation": "Mes1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.909243, "sdRefIntergenicDistribution": 1.844968, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 164529, "distinctRankCount": 602, "maxRank": 23615.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0008019", "name": "mesenchymal cell" }, "cellTypeAuthorAnnotation": "Mes2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 17.314818, "sdRefIntergenicDistribution": 1.685141, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 70377, "distinctRankCount": 444, "maxRank": 22150.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000127", "name": "astrocyte" }, "cellTypeAuthorAnnotation": "Astro1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.555001, "sdRefIntergenicDistribution": 2.588980, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 826105, "distinctRankCount": 1570, "maxRank": 25278.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000127", "name": "astrocyte" }, "cellTypeAuthorAnnotation": "Astro2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 16.470044, "sdRefIntergenicDistribution": 1.777029, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 74822, "distinctRankCount": 428, "maxRank": 22590.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000127", "name": "astrocyte" }, "cellTypeAuthorAnnotation": "Astro3", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.037549, "sdRefIntergenicDistribution": 1.919575, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 166468, "distinctRankCount": 416, "maxRank": 23393.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000071", "name": "blood vessel endothelial cell" }, "cellTypeAuthorAnnotation": "EC1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.755830, "sdRefIntergenicDistribution": 2.257011, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 634056, "distinctRankCount": 1349, "maxRank": 24948.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000071", "name": "blood vessel endothelial cell" }, "cellTypeAuthorAnnotation": "EC2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.478867, "sdRefIntergenicDistribution": 1.821288, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 87159, "distinctRankCount": 422, "maxRank": 22945.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Mφ", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.198635, "sdRefIntergenicDistribution": 1.884248, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 144249, "distinctRankCount": 600, "maxRank": 23322.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0002453", "name": "oligodendrocyte precursor cell" }, "cellTypeAuthorAnnotation": "OPC", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.563833, "sdRefIntergenicDistribution": 1.919393, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 180308, "distinctRankCount": 953, "maxRank": 23901.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000576", "name": "monocyte" }, "cellTypeAuthorAnnotation": "Mono", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.679632, "sdRefIntergenicDistribution": 1.892018, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 205564, "distinctRankCount": 762, "maxRank": 23872.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0008034", "name": "mural cell" }, "cellTypeAuthorAnnotation": "Mural1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 24.490267, "sdRefIntergenicDistribution": 1.653026, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 47267, "distinctRankCount": 396, "maxRank": 22016.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0008034", "name": "mural cell" }, "cellTypeAuthorAnnotation": "Mural2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.547129, "sdRefIntergenicDistribution": 1.896921, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 176230, "distinctRankCount": 688, "maxRank": 23827.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000232", "name": "erythrocyte" }, "cellTypeAuthorAnnotation": "RBCs", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 25.254757, "sdRefIntergenicDistribution": 1.688585, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 48324, "distinctRankCount": 63, "maxRank": 18986.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 502892201, "mappedReadsCount": 288088908, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947725" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000128", "name": "oligodendrocyte" }, "cellTypeAuthorAnnotation": "MyOligo", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.279513, "sdRefIntergenicDistribution": 2.126538, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 362886, "distinctRankCount": 1189, "maxRank": 23984.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0011028", "name": "olfactory ensheathing cell" }, "cellTypeAuthorAnnotation": "OEC1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.153019, "sdRefIntergenicDistribution": 2.667409, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1080308, "distinctRankCount": 1726, "maxRank": 25420.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0011028", "name": "olfactory ensheathing cell" }, "cellTypeAuthorAnnotation": "OEC2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.376336, "sdRefIntergenicDistribution": 2.559030, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 909389, "distinctRankCount": 1595, "maxRank": 25255.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0011028", "name": "olfactory ensheathing cell" }, "cellTypeAuthorAnnotation": "OEC3", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.023809, "sdRefIntergenicDistribution": 2.202564, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 553435, "distinctRankCount": 953, "maxRank": 24871.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0011028", "name": "olfactory ensheathing cell" }, "cellTypeAuthorAnnotation": "OEC4", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.779079, "sdRefIntergenicDistribution": 2.717149, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1385177, "distinctRankCount": 1891, "maxRank": 25558.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0011028", "name": "olfactory ensheathing cell" }, "cellTypeAuthorAnnotation": "OEC5", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.153146, "sdRefIntergenicDistribution": 2.166879, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 392575, "distinctRankCount": 998, "maxRank": 24444.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000129", "name": "microglial cell" }, "cellTypeAuthorAnnotation": "MicroG1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.440723, "sdRefIntergenicDistribution": 2.169763, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 292218, "distinctRankCount": 891, "maxRank": 24052.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000129", "name": "microglial cell" }, "cellTypeAuthorAnnotation": "MicroG2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.596878, "sdRefIntergenicDistribution": 2.551425, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 805743, "distinctRankCount": 1470, "maxRank": 25109.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000129", "name": "microglial cell" }, "cellTypeAuthorAnnotation": "MicroG3", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.290818, "sdRefIntergenicDistribution": 1.842979, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 127598, "distinctRankCount": 368, "maxRank": 22855.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.269712, "sdRefIntergenicDistribution": 2.730850, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1089753, "distinctRankCount": 1808, "maxRank": 25522.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N10", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.412641, "sdRefIntergenicDistribution": 2.730360, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1022140, "distinctRankCount": 2109, "maxRank": 25556.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N11", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.901122, "sdRefIntergenicDistribution": 2.852504, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 623873, "distinctRankCount": 3033, "maxRank": 25837.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N12", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.668031, "sdRefIntergenicDistribution": 2.254169, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 359747, "distinctRankCount": 1123, "maxRank": 24791.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N13", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.226834, "sdRefIntergenicDistribution": 2.716151, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1107024, "distinctRankCount": 1841, "maxRank": 25603.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N14", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.565093, "sdRefIntergenicDistribution": 2.003080, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 161996, "distinctRankCount": 1173, "maxRank": 23887.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N15", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.703134, "sdRefIntergenicDistribution": 2.007285, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 249060, "distinctRankCount": 632, "maxRank": 24111.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N16", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.342961, "sdRefIntergenicDistribution": 1.881029, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 143097, "distinctRankCount": 870, "maxRank": 23362.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 16.312988, "sdRefIntergenicDistribution": 1.782465, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 76267, "distinctRankCount": 607, "maxRank": 22685.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N3", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.192347, "sdRefIntergenicDistribution": 1.768959, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 115471, "distinctRankCount": 595, "maxRank": 22851.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N4", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.470621, "sdRefIntergenicDistribution": 1.923308, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 114620, "distinctRankCount": 774, "maxRank": 23191.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N5", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.097893, "sdRefIntergenicDistribution": 2.106246, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 239397, "distinctRankCount": 375, "maxRank": 23044.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N6", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.241422, "sdRefIntergenicDistribution": 2.285833, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 482820, "distinctRankCount": 647, "maxRank": 24605.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N7", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.413526, "sdRefIntergenicDistribution": 1.901542, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 127637, "distinctRankCount": 346, "maxRank": 22950.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N8", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.169845, "sdRefIntergenicDistribution": 2.931851, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 809638, "distinctRankCount": 1559, "maxRank": 25596.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N9", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.737575, "sdRefIntergenicDistribution": 2.543551, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 392888, "distinctRankCount": 1114, "maxRank": 25102.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0008019", "name": "mesenchymal cell" }, "cellTypeAuthorAnnotation": "Mes1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.863160, "sdRefIntergenicDistribution": 1.930484, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 240096, "distinctRankCount": 844, "maxRank": 24174.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0008019", "name": "mesenchymal cell" }, "cellTypeAuthorAnnotation": "Mes2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.418636, "sdRefIntergenicDistribution": 1.775061, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 124304, "distinctRankCount": 773, "maxRank": 23194.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000127", "name": "astrocyte" }, "cellTypeAuthorAnnotation": "Astro1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 1.956098, "sdRefIntergenicDistribution": 2.804421, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1359492, "distinctRankCount": 1971, "maxRank": 25762.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000127", "name": "astrocyte" }, "cellTypeAuthorAnnotation": "Astro2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.892106, "sdRefIntergenicDistribution": 1.919821, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 153405, "distinctRankCount": 654, "maxRank": 23625.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000127", "name": "astrocyte" }, "cellTypeAuthorAnnotation": "Astro3", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.355541, "sdRefIntergenicDistribution": 1.991388, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 266542, "distinctRankCount": 591, "maxRank": 24163.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000071", "name": "blood vessel endothelial cell" }, "cellTypeAuthorAnnotation": "EC1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.169603, "sdRefIntergenicDistribution": 2.414709, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 909908, "distinctRankCount": 1701, "maxRank": 25336.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000071", "name": "blood vessel endothelial cell" }, "cellTypeAuthorAnnotation": "EC2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.286992, "sdRefIntergenicDistribution": 1.994331, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 274813, "distinctRankCount": 837, "maxRank": 24403.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Mφ", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.377135, "sdRefIntergenicDistribution": 1.931127, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 187154, "distinctRankCount": 642, "maxRank": 23682.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0002453", "name": "oligodendrocyte precursor cell" }, "cellTypeAuthorAnnotation": "OPC", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.033101, "sdRefIntergenicDistribution": 2.043746, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 250460, "distinctRankCount": 1239, "maxRank": 24291.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000576", "name": "monocyte" }, "cellTypeAuthorAnnotation": "Mono", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.028112, "sdRefIntergenicDistribution": 1.977560, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 293976, "distinctRankCount": 956, "maxRank": 24386.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0008034", "name": "mural cell" }, "cellTypeAuthorAnnotation": "Mural1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 13.892672, "sdRefIntergenicDistribution": 1.735851, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 89981, "distinctRankCount": 629, "maxRank": 22979.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0008034", "name": "mural cell" }, "cellTypeAuthorAnnotation": "Mural2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.092480, "sdRefIntergenicDistribution": 1.990001, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 237802, "distinctRankCount": 796, "maxRank": 24242.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000232", "name": "erythrocyte" }, "cellTypeAuthorAnnotation": "RBCs", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.969660, "sdRefIntergenicDistribution": 1.778196, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 267210, "distinctRankCount": 261, "maxRank": 21855.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 546829212, "mappedReadsCount": 341527518, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947726" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000128", "name": "oligodendrocyte" }, "cellTypeAuthorAnnotation": "MyOligo", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.928954, "sdRefIntergenicDistribution": 2.315436, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 622232, "distinctRankCount": 1565, "maxRank": 24636.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0011028", "name": "olfactory ensheathing cell" }, "cellTypeAuthorAnnotation": "OEC1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.651293, "sdRefIntergenicDistribution": 2.530253, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 770303, "distinctRankCount": 1539, "maxRank": 25121.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0011028", "name": "olfactory ensheathing cell" }, "cellTypeAuthorAnnotation": "OEC2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.841430, "sdRefIntergenicDistribution": 2.515917, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 701715, "distinctRankCount": 1452, "maxRank": 24950.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0011028", "name": "olfactory ensheathing cell" }, "cellTypeAuthorAnnotation": "OEC3", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.305417, "sdRefIntergenicDistribution": 2.241880, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 501260, "distinctRankCount": 936, "maxRank": 24812.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0011028", "name": "olfactory ensheathing cell" }, "cellTypeAuthorAnnotation": "OEC4", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.070498, "sdRefIntergenicDistribution": 2.678649, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 1102926, "distinctRankCount": 1668, "maxRank": 25327.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0011028", "name": "olfactory ensheathing cell" }, "cellTypeAuthorAnnotation": "OEC5", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.403087, "sdRefIntergenicDistribution": 2.124015, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 285728, "distinctRankCount": 882, "maxRank": 23995.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000129", "name": "microglial cell" }, "cellTypeAuthorAnnotation": "MicroG1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.724482, "sdRefIntergenicDistribution": 2.306584, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 357198, "distinctRankCount": 1033, "maxRank": 24139.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000129", "name": "microglial cell" }, "cellTypeAuthorAnnotation": "MicroG2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.975065, "sdRefIntergenicDistribution": 2.561325, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 683027, "distinctRankCount": 1322, "maxRank": 24971.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000129", "name": "microglial cell" }, "cellTypeAuthorAnnotation": "MicroG3", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 12.311992, "sdRefIntergenicDistribution": 2.004620, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 111319, "distinctRankCount": 317, "maxRank": 22644.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.955703, "sdRefIntergenicDistribution": 2.530907, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 701359, "distinctRankCount": 1482, "maxRank": 25034.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N10", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.384083, "sdRefIntergenicDistribution": 2.532472, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 581859, "distinctRankCount": 1570, "maxRank": 24970.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N11", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.539753, "sdRefIntergenicDistribution": 2.759553, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 452550, "distinctRankCount": 2255, "maxRank": 25472.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N12", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.352785, "sdRefIntergenicDistribution": 2.221341, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 295836, "distinctRankCount": 1071, "maxRank": 24516.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N13", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.871338, "sdRefIntergenicDistribution": 2.561237, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 722923, "distinctRankCount": 1518, "maxRank": 25190.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N14", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.543147, "sdRefIntergenicDistribution": 2.086683, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 161649, "distinctRankCount": 1334, "maxRank": 24010.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N15", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 7.958530, "sdRefIntergenicDistribution": 1.991995, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 172975, "distinctRankCount": 529, "maxRank": 23588.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N16", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.742959, "sdRefIntergenicDistribution": 1.939750, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 138073, "distinctRankCount": 864, "maxRank": 23299.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 47.576223, "sdRefIntergenicDistribution": 1.655680, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 23165, "distinctRankCount": 264, "maxRank": 20870.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N3", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 18.610711, "sdRefIntergenicDistribution": 1.808450, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 68364, "distinctRankCount": 430, "maxRank": 22104.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N4", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 37.771806, "sdRefIntergenicDistribution": 1.710052, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 28801, "distinctRankCount": 306, "maxRank": 21233.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N5", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 8.009200, "sdRefIntergenicDistribution": 2.077789, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 179289, "distinctRankCount": 326, "maxRank": 22387.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N6", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.033865, "sdRefIntergenicDistribution": 2.236583, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 297986, "distinctRankCount": 504, "maxRank": 24042.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N7", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 17.982151, "sdRefIntergenicDistribution": 1.948891, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 73543, "distinctRankCount": 251, "maxRank": 22044.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N8", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 4.019033, "sdRefIntergenicDistribution": 2.789106, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 524281, "distinctRankCount": 1325, "maxRank": 25116.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000540", "name": "neuron" }, "cellTypeAuthorAnnotation": "N9", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.071106, "sdRefIntergenicDistribution": 2.577181, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 345259, "distinctRankCount": 1090, "maxRank": 24972.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0008019", "name": "mesenchymal cell" }, "cellTypeAuthorAnnotation": "Mes1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.476518, "sdRefIntergenicDistribution": 1.884017, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 138649, "distinctRankCount": 525, "maxRank": 23410.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0008019", "name": "mesenchymal cell" }, "cellTypeAuthorAnnotation": "Mes2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 10.351507, "sdRefIntergenicDistribution": 1.839836, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 128891, "distinctRankCount": 872, "maxRank": 23164.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000127", "name": "astrocyte" }, "cellTypeAuthorAnnotation": "Astro1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.422494, "sdRefIntergenicDistribution": 2.693174, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 936758, "distinctRankCount": 1605, "maxRank": 25368.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000127", "name": "astrocyte" }, "cellTypeAuthorAnnotation": "Astro2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 11.794691, "sdRefIntergenicDistribution": 1.890943, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 110543, "distinctRankCount": 565, "maxRank": 23145.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000127", "name": "astrocyte" }, "cellTypeAuthorAnnotation": "Astro3", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.699981, "sdRefIntergenicDistribution": 2.042469, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 208735, "distinctRankCount": 485, "maxRank": 23741.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000071", "name": "blood vessel endothelial cell" }, "cellTypeAuthorAnnotation": "EC1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 2.342961, "sdRefIntergenicDistribution": 2.432963, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 819822, "distinctRankCount": 1472, "maxRank": 25158.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000071", "name": "blood vessel endothelial cell" }, "cellTypeAuthorAnnotation": "EC2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.692402, "sdRefIntergenicDistribution": 1.977552, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 206197, "distinctRankCount": 681, "maxRank": 24083.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000235", "name": "macrophage" }, "cellTypeAuthorAnnotation": "Mφ", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 9.786343, "sdRefIntergenicDistribution": 1.904683, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 136369, "distinctRankCount": 552, "maxRank": 23266.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0002453", "name": "oligodendrocyte precursor cell" }, "cellTypeAuthorAnnotation": "OPC", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.952851, "sdRefIntergenicDistribution": 2.029019, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 209211, "distinctRankCount": 1055, "maxRank": 24074.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000576", "name": "monocyte" }, "cellTypeAuthorAnnotation": "Mono", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 5.308939, "sdRefIntergenicDistribution": 2.013552, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 277042, "distinctRankCount": 942, "maxRank": 24153.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0008034", "name": "mural cell" }, "cellTypeAuthorAnnotation": "Mural1", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 14.101755, "sdRefIntergenicDistribution": 1.777475, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 89032, "distinctRankCount": 578, "maxRank": 22825.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0008034", "name": "mural cell" }, "cellTypeAuthorAnnotation": "Mural2", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 6.375524, "sdRefIntergenicDistribution": 2.012409, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 223701, "distinctRankCount": 811, "maxRank": 24135.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000232", "name": "erythrocyte" }, "cellTypeAuthorAnnotation": "RBCs", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 17.451181, "sdRefIntergenicDistribution": 1.746241, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 72921, "distinctRankCount": 105, "maxRank": 19861.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "NextSeq 500", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 547582565, "mappedReadsCount": 336194295, "minReadLength": 66, "maxReadLength": 66 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 34984, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Mus", "speciesName": "musculus", "genomeVersion": "GRCm38.p6", "speciesFullNameWithoutSpace": "Mus_musculus", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Mus_musculus/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 862507, "genomeSpeciesId": 10090, "preferredDisplayOrder": 2, "name": "mouse", "id": 10090 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/", "fileName": "Mus_musculus_SRP167086_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "size": 0 } ], "dataSource": { "xRefUrl": "", "experimentUrl": "https://www.ncbi.nlm.nih.gov/sra/[experiment_id]", "evidenceUrl": "https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=[evidence_id]", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/", "releaseDate": "2023-04-04", "releaseVersion": "", "toDisplay": true, "category": "SC_RNA_SEQ", "displayOrder": 1, "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "id": 102 }, "xRef": { "xRefId": "SRP167086", "xRefName": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP167086", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1038/s41467-021-25444-3", "name": "Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons", "description": "Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system. Overall design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.", "id": "SRP167086" }, "id": "SRX4947727" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:0002264", "name": "olfactory bulb" }, "anatEntityAuthorAnnotation": "Olfactory bulb", "cellType": { "id": "CL:0000128", "name": "oligodendrocyte" }, "cellTypeAuthorAnnotation": "MyOligo", "devStage": { "id": "MmusDv:0000137", "name": "3-6 month-old mature stage (mouse)" }, "devStageAuthorAnnotation": "14-20 weeks", "sex": "mixed", "strain": "C57BL/6NJ", "time": "NA", "timeUnit": "NA", "species": { "id": 10090, "name": "mouse", "genus": "Mus", "speciesName": "musculus", "preferredDisplayOrder": 2 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 3.608493, "sdRefIntergenicDistribution": 2.270850, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 474491, "distinctRankCount": 1361, "maxRank": 24350.00 }, "barcode": "" } ], "downloadUrls": [ { "text": "scRNA-Seq droplet-based processed expression values per cell population in Mus musculus", "href": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Mus_musculus/Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz", "title": "Mus_musculus_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP167086.tsv.gz" }, { "text": "scRNA-Seq droplet-based H5AD data per cell in Mus musculus", "href": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Mus_musculus/Mus_musculus_SRP167086_droplet_based.h5ad", "title": "Mus_musculus_SRP167086_droplet_based.h5ad" } ] } }