{ "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": 6092, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Drosophila", "speciesName": "melanogaster", "genomeVersion": "BDGP6.28", "speciesFullNameWithoutSpace": "Drosophila_melanogaster", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Drosophila_melanogaster/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 32351, "genomeSpeciesId": 7227, "preferredDisplayOrder": 4, "name": "fruit fly", "id": 7227 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Drosophila_melanogaster/", "fileName": "Drosophila_melanogaster_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP269777.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Drosophila melanogaster", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Drosophila", "speciesName": "melanogaster", "genomeVersion": "BDGP6.28", "speciesFullNameWithoutSpace": "Drosophila_melanogaster", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Drosophila_melanogaster/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 32351, "genomeSpeciesId": 7227, "preferredDisplayOrder": 4, "name": "fruit fly", "id": 7227 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Drosophila_melanogaster/", "fileName": "Drosophila_melanogaster_SRP269777_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Drosophila melanogaster", "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": "SRP269777", "xRefName": "The molecular landscape of neural differentiation inthe developing Drosophila brain revealed by targeted scRNA-seq and multi-informatic analysis", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP269777", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1016/j.celrep.2021.109039", "name": "The molecular landscape of neural differentiation inthe developing Drosophila brain revealed by targeted scRNA-seq and multi-informatic analysis", "description": "In this work, Michki et. al. isolate neurons and neural progenitors from the developing Drosophila brain. Through a combination of in silico and in situ techniques, they map out the expression dynamics of a variety of molecular factors that may play a role in specifying terminal neural fates at the RNA level, and provide tools to enable similar analyses to be performed in other systems. Overall design: R9D11-Gal4 genetic driver was used with a UAS:hH2B-2xmNG reporter to label type-II neural lineages in third instar larval brains. 20 brains were dissected, dissociated, and sorted on a Sony MA900 FACS machine. 10,000 cells were sequenced in a single lane of a 10Xchromium chip using their v3 chemistry. Cells were sequenced on an Illumina NovaSeq/HiSeq4000 with 400M reads allocated to this library. 6092 cells were identified with a mean read count of 97,604 reads/cell when aligned to the BDGP6(2014-07) Drosophila genome assembly from ENSEMBL using STAR. Downstream filtering and analysis were performed using scanpy.", "id": "SRP269777" }, "assays": [ { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina NovaSeq 6000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 384758486, "mappedReadsCount": 348924578, "minReadLength": 110, "maxReadLength": 110 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 6092, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Drosophila", "speciesName": "melanogaster", "genomeVersion": "BDGP6.28", "speciesFullNameWithoutSpace": "Drosophila_melanogaster", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Drosophila_melanogaster/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 32351, "genomeSpeciesId": 7227, "preferredDisplayOrder": 4, "name": "fruit fly", "id": 7227 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Drosophila_melanogaster/", "fileName": "Drosophila_melanogaster_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP269777.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Drosophila melanogaster", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Drosophila", "speciesName": "melanogaster", "genomeVersion": "BDGP6.28", "speciesFullNameWithoutSpace": "Drosophila_melanogaster", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Drosophila_melanogaster/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 32351, "genomeSpeciesId": 7227, "preferredDisplayOrder": 4, "name": "fruit fly", "id": 7227 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Drosophila_melanogaster/", "fileName": "Drosophila_melanogaster_SRP269777_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Drosophila melanogaster", "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": "SRP269777", "xRefName": "The molecular landscape of neural differentiation inthe developing Drosophila brain revealed by targeted scRNA-seq and multi-informatic analysis", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP269777", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1016/j.celrep.2021.109039", "name": "The molecular landscape of neural differentiation inthe developing Drosophila brain revealed by targeted scRNA-seq and multi-informatic analysis", "description": "In this work, Michki et. al. isolate neurons and neural progenitors from the developing Drosophila brain. Through a combination of in silico and in situ techniques, they map out the expression dynamics of a variety of molecular factors that may play a role in specifying terminal neural fates at the RNA level, and provide tools to enable similar analyses to be performed in other systems. Overall design: R9D11-Gal4 genetic driver was used with a UAS:hH2B-2xmNG reporter to label type-II neural lineages in third instar larval brains. 20 brains were dissected, dissociated, and sorted on a Sony MA900 FACS machine. 10,000 cells were sequenced in a single lane of a 10Xchromium chip using their v3 chemistry. Cells were sequenced on an Illumina NovaSeq/HiSeq4000 with 400M reads allocated to this library. 6092 cells were identified with a mean read count of 97,604 reads/cell when aligned to the BDGP6(2014-07) Drosophila genome assembly from ENSEMBL using STAR. Downstream filtering and analysis were performed using scanpy.", "id": "SRP269777" }, "id": "SRX8657660" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:6001920", "name": "insect embryonic/larval brain" }, "anatEntityAuthorAnnotation": "brain", "cellType": { "id": "FBbt:00100533", "name": "type II neuroblast (Drosophila)" }, "cellTypeAuthorAnnotation": "typeII", "devStage": { "id": "FBdv:00007007", "name": "late third instar larval stage (fruit fly)" }, "devStageAuthorAnnotation": "3rd instar larva", "sex": "NA", "strain": "[;;R9D11-Gal4/UAS-hH2B::2xmNG]", "time": "NA", "timeUnit": "NA", "species": { "id": 7227, "name": "fruit fly", "genus": "Drosophila", "speciesName": "melanogaster", "preferredDisplayOrder": 4 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.161437, "sdRefIntergenicDistribution": 3.676995, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 30678604, "distinctRankCount": 3820, "maxRank": 12786.50 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V3", "sequencingPlatfomName": "Illumina NovaSeq 6000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 384758486, "mappedReadsCount": 348924578, "minReadLength": 110, "maxReadLength": 110 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 6092, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Drosophila", "speciesName": "melanogaster", "genomeVersion": "BDGP6.28", "speciesFullNameWithoutSpace": "Drosophila_melanogaster", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Drosophila_melanogaster/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 32351, "genomeSpeciesId": 7227, "preferredDisplayOrder": 4, "name": "fruit fly", "id": 7227 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Drosophila_melanogaster/", "fileName": "Drosophila_melanogaster_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP269777.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Drosophila melanogaster", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Drosophila", "speciesName": "melanogaster", "genomeVersion": "BDGP6.28", "speciesFullNameWithoutSpace": "Drosophila_melanogaster", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Drosophila_melanogaster/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 32351, "genomeSpeciesId": 7227, "preferredDisplayOrder": 4, "name": "fruit fly", "id": 7227 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Drosophila_melanogaster/", "fileName": "Drosophila_melanogaster_SRP269777_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Drosophila melanogaster", "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": "SRP269777", "xRefName": "The molecular landscape of neural differentiation inthe developing Drosophila brain revealed by targeted scRNA-seq and multi-informatic analysis", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP269777", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1016/j.celrep.2021.109039", "name": "The molecular landscape of neural differentiation inthe developing Drosophila brain revealed by targeted scRNA-seq and multi-informatic analysis", "description": "In this work, Michki et. al. isolate neurons and neural progenitors from the developing Drosophila brain. Through a combination of in silico and in situ techniques, they map out the expression dynamics of a variety of molecular factors that may play a role in specifying terminal neural fates at the RNA level, and provide tools to enable similar analyses to be performed in other systems. Overall design: R9D11-Gal4 genetic driver was used with a UAS:hH2B-2xmNG reporter to label type-II neural lineages in third instar larval brains. 20 brains were dissected, dissociated, and sorted on a Sony MA900 FACS machine. 10,000 cells were sequenced in a single lane of a 10Xchromium chip using their v3 chemistry. Cells were sequenced on an Illumina NovaSeq/HiSeq4000 with 400M reads allocated to this library. 6092 cells were identified with a mean read count of 97,604 reads/cell when aligned to the BDGP6(2014-07) Drosophila genome assembly from ENSEMBL using STAR. Downstream filtering and analysis were performed using scanpy.", "id": "SRP269777" }, "id": "SRX8657660" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:6001920", "name": "insect embryonic/larval brain" }, "anatEntityAuthorAnnotation": "brain", "cellType": { "id": "FBbt:00110571", "name": "optic lobe forming neuroblast (Drosophila)" }, "cellTypeAuthorAnnotation": "OL", "devStage": { "id": "FBdv:00007007", "name": "late third instar larval stage (fruit fly)" }, "devStageAuthorAnnotation": "3rd instar larva", "sex": "NA", "strain": "[;;R9D11-Gal4/UAS-hH2B::2xmNG]", "time": "NA", "timeUnit": "NA", "species": { "id": 7227, "name": "fruit fly", "genus": "Drosophila", "speciesName": "melanogaster", "preferredDisplayOrder": 4 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.146599, "sdRefIntergenicDistribution": 3.388194, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 27212561, "distinctRankCount": 3342, "maxRank": 12956.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 381823225, "mappedReadsCount": 352134454, "minReadLength": 115, "maxReadLength": 115 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 6092, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Drosophila", "speciesName": "melanogaster", "genomeVersion": "BDGP6.28", "speciesFullNameWithoutSpace": "Drosophila_melanogaster", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Drosophila_melanogaster/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 32351, "genomeSpeciesId": 7227, "preferredDisplayOrder": 4, "name": "fruit fly", "id": 7227 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Drosophila_melanogaster/", "fileName": "Drosophila_melanogaster_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP269777.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Drosophila melanogaster", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Drosophila", "speciesName": "melanogaster", "genomeVersion": "BDGP6.28", "speciesFullNameWithoutSpace": "Drosophila_melanogaster", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Drosophila_melanogaster/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 32351, "genomeSpeciesId": 7227, "preferredDisplayOrder": 4, "name": "fruit fly", "id": 7227 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Drosophila_melanogaster/", "fileName": "Drosophila_melanogaster_SRP269777_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Drosophila melanogaster", "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": "SRP269777", "xRefName": "The molecular landscape of neural differentiation inthe developing Drosophila brain revealed by targeted scRNA-seq and multi-informatic analysis", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP269777", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1016/j.celrep.2021.109039", "name": "The molecular landscape of neural differentiation inthe developing Drosophila brain revealed by targeted scRNA-seq and multi-informatic analysis", "description": "In this work, Michki et. al. isolate neurons and neural progenitors from the developing Drosophila brain. Through a combination of in silico and in situ techniques, they map out the expression dynamics of a variety of molecular factors that may play a role in specifying terminal neural fates at the RNA level, and provide tools to enable similar analyses to be performed in other systems. Overall design: R9D11-Gal4 genetic driver was used with a UAS:hH2B-2xmNG reporter to label type-II neural lineages in third instar larval brains. 20 brains were dissected, dissociated, and sorted on a Sony MA900 FACS machine. 10,000 cells were sequenced in a single lane of a 10Xchromium chip using their v3 chemistry. Cells were sequenced on an Illumina NovaSeq/HiSeq4000 with 400M reads allocated to this library. 6092 cells were identified with a mean read count of 97,604 reads/cell when aligned to the BDGP6(2014-07) Drosophila genome assembly from ENSEMBL using STAR. Downstream filtering and analysis were performed using scanpy.", "id": "SRP269777" }, "id": "SRX9904377" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:6001920", "name": "insect embryonic/larval brain" }, "anatEntityAuthorAnnotation": "brain", "cellType": { "id": "FBbt:00100533", "name": "type II neuroblast (Drosophila)" }, "cellTypeAuthorAnnotation": "typeII", "devStage": { "id": "FBdv:00007007", "name": "late third instar larval stage (fruit fly)" }, "devStageAuthorAnnotation": "3rd instar larva", "sex": "NA", "strain": "[;;R9D11-Gal4/UAS-hH2B::2xmNG]", "time": "NA", "timeUnit": "NA", "species": { "id": 7227, "name": "fruit fly", "genus": "Drosophila", "speciesName": "melanogaster", "preferredDisplayOrder": 4 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.186034, "sdRefIntergenicDistribution": 3.435754, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 20292362, "distinctRankCount": 3253, "maxRank": 12347.00 }, "barcode": "" }, { "library": { "technology": { "protocolName": "10X Genomics V2", "sequencingPlatfomName": "Illumina HiSeq 4000", "strand": "NA", "sequencedTranscriptPart": "THREE_PRIME", "cellCompartment": "CELL", "isSampleMultiplexing": true, "isLibraryMultiplexing": false, "fragmentation": 0, "libraryType": "paired" }, "pipelineSummary": { "allReadsCount": 381823225, "mappedReadsCount": 352134454, "minReadLength": 115, "maxReadLength": 115 }, "experiment": { "sampleMultiplexing": true, "numberOfAnnotatedCells": 6092, "downloadFiles": [ { "category": "ANNOTATED_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Drosophila", "speciesName": "melanogaster", "genomeVersion": "BDGP6.28", "speciesFullNameWithoutSpace": "Drosophila_melanogaster", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Drosophila_melanogaster/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 32351, "genomeSpeciesId": 7227, "preferredDisplayOrder": 4, "name": "fruit fly", "id": 7227 }, "path": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Drosophila_melanogaster/", "fileName": "Drosophila_melanogaster_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP269777.tsv.gz", "title": "scRNA-Seq droplet-based processed expression values per cell population in Drosophila melanogaster", "size": 0 }, { "category": "INDIVIDUAL_SAMPLES", "dataType": "SC_RNA_SEQ", "sampleMultiplexing": true, "species": { "genus": "Drosophila", "speciesName": "melanogaster", "genomeVersion": "BDGP6.28", "speciesFullNameWithoutSpace": "Drosophila_melanogaster", "genomeAssemblyXRef": "https://nov2020.archive.ensembl.org/Drosophila_melanogaster/", "dataSourcesForDataByDataTypes": {}, "dataSourcesForAnnotationByDataTypes": {}, "parentTaxonId": 32351, "genomeSpeciesId": 7227, "preferredDisplayOrder": 4, "name": "fruit fly", "id": 7227 }, "path": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Drosophila_melanogaster/", "fileName": "Drosophila_melanogaster_SRP269777_droplet_based.h5ad", "title": "scRNA-Seq droplet-based H5AD data per cell in Drosophila melanogaster", "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": "SRP269777", "xRefName": "The molecular landscape of neural differentiation inthe developing Drosophila brain revealed by targeted scRNA-seq and multi-informatic analysis", "xRefURL": "https://www.ncbi.nlm.nih.gov/sra/SRP269777", "source": { "name": "SRA", "description": "Single-cell RNA-Seq data source for various species", "baseUrl": "https://www.ncbi.nlm.nih.gov/sra/" } }, "assayCount": 0, "dOI": "10.1016/j.celrep.2021.109039", "name": "The molecular landscape of neural differentiation inthe developing Drosophila brain revealed by targeted scRNA-seq and multi-informatic analysis", "description": "In this work, Michki et. al. isolate neurons and neural progenitors from the developing Drosophila brain. Through a combination of in silico and in situ techniques, they map out the expression dynamics of a variety of molecular factors that may play a role in specifying terminal neural fates at the RNA level, and provide tools to enable similar analyses to be performed in other systems. Overall design: R9D11-Gal4 genetic driver was used with a UAS:hH2B-2xmNG reporter to label type-II neural lineages in third instar larval brains. 20 brains were dissected, dissociated, and sorted on a Sony MA900 FACS machine. 10,000 cells were sequenced in a single lane of a 10Xchromium chip using their v3 chemistry. Cells were sequenced on an Illumina NovaSeq/HiSeq4000 with 400M reads allocated to this library. 6092 cells were identified with a mean read count of 97,604 reads/cell when aligned to the BDGP6(2014-07) Drosophila genome assembly from ENSEMBL using STAR. Downstream filtering and analysis were performed using scanpy.", "id": "SRP269777" }, "id": "SRX9904377" }, "annotation": { "rawDataCondition": { "anatEntity": { "id": "UBERON:6001920", "name": "insect embryonic/larval brain" }, "anatEntityAuthorAnnotation": "brain", "cellType": { "id": "FBbt:00110571", "name": "optic lobe forming neuroblast (Drosophila)" }, "cellTypeAuthorAnnotation": "OL", "devStage": { "id": "FBdv:00007007", "name": "late third instar larval stage (fruit fly)" }, "devStageAuthorAnnotation": "3rd instar larva", "sex": "NA", "strain": "[;;R9D11-Gal4/UAS-hH2B::2xmNG]", "time": "NA", "timeUnit": "NA", "species": { "id": 7227, "name": "fruit fly", "genus": "Drosophila", "speciesName": "melanogaster", "preferredDisplayOrder": 4 } }, "physiologicalStatus": "NA" }, "pipelineSummary": { "meanRefIntergenicDistribution": 0.419247, "sdRefIntergenicDistribution": 2.718621, "pValueThreshold": 0.0500, "allUMIsCount": 0, "mappedUMIsCount": 5904322, "distinctRankCount": 1817, "maxRank": 11849.00 }, "barcode": "" } ], "downloadUrls": [ { "text": "scRNA-Seq droplet-based processed expression values per cell population in Drosophila melanogaster", "href": "https://www.bgee.org/ftp/current/download/processed_expr_values/droplet_based/Drosophila_melanogaster/Drosophila_melanogaster_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP269777.tsv.gz", "title": "Drosophila_melanogaster_Droplet-Based_SC_RNA-Seq_read_counts_CPM_SRP269777.tsv.gz" }, { "text": "scRNA-Seq droplet-based H5AD data per cell in Drosophila melanogaster", "href": "https://www.bgee.org/ftp/current/download/h5ad/droplet_based/Drosophila_melanogaster/Drosophila_melanogaster_SRP269777_droplet_based.h5ad", "title": "Drosophila_melanogaster_SRP269777_droplet_based.h5ad" } ] } }