{"database": "metadata", "table": "run_metadata", "rows": [[59864, "SRR12054791", "SRX8583210", "SRS6874827", "SRP268010", "PRJNA640615", "Molecular classification of zebrafish retinal ganglion cells links genes to behavior", "GSE152842", "Transcriptome Analysis", "Retinal ganglion cells RGCs form an array of feature detectors  which transmit visual information through segregated channels to central brain regions. Characterizing RGC diversity is required to understand the logic of this functional parcellation. Using single  cell transcriptomics  we systematically classified RGCs in adult and larval zebrafish  thereby identifying marker genes for >30 stable and several transient cell types  cell type specific markers  and their maturational changes. We used this catalog to engineer transgenic driverreporter lines  enabling experimental genetic access to specific RGC types. Strikingly  expression of a few transcription factors often predicts dendrite morphological features  in particular and axonal projections to specific tectal layers and extratectal targets. Moreover  iIn vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuningphysiological properties. Finally  chemogenetic ablation of eomesa+ RGCs  which comprise three melanopsin expressing types with a specific projections to thalamus  pretectum and one deep tectal layerpattern  selectively impaired a visual behavior  phototaxis. Our study establishes a framework and provides a resource for systematically studying the functional architecture of the visual system. Overall design: RGCs were labeled using transgenic Tgisl2b:tagRFP zebrafish that express RFP in all RGCs. Retinas from larval 5 dpf and adult 4 month 6 month fish were dissected and sorted using FACS. For the larval dataset  200 manually dissected retinas were dissociated in one experiment and single cell profiles were collected across 3 replicates. For the adult dataset  about 20 retinas per batch were dissected and dissociated and droplet RNA sequencing was performed collecting a total of 15 replicates across 5 experiments. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell.", null, "pubmed:33357413", null, "Adult Zebrafish 8", "GSM4627220", null, "source name:Zebrafish retina  4 mpf 6 mpf|tissue:retina", "Adult Zebrafish 8", "Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger softwareversion 2.1.0  10X Genomics Sample alignment to the zebrafish reference transcriptome ENSEMBL zv10  release 82 using \u201ccellranger count\u201d with default parameters to obtain a digital gene expression DGE matrix genes x cells summarizing transcript counts. Genome build: ENSEMBL zv10  release 82 Supplementary files format and content: Csv files including gene expression matrix from all larval samples and all adult samples", "Zebrafish retina  4 mpf 6 mpf", "All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated ox Ames and transferred into ox Ames on ice until tissue collection was completed.", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion  the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension  cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium 3\u2019 v2 platform 10X Genomics  Pleasanton  CA", "Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28\u00b0C. Embryos were bred in Danieau\u2019s solution 17 mM NaCl  2 mM KCl  0.12 mM MgSO4  1.8 mM CaNO32  1.5 mM HEPES.", "tissue:retina", "GSM4627220", "GSM4627220: Adult Zebrafish 8; Danio rerio; RNA Seq", "GSM4627220", null, "1", "Retinas were digested in papain 20U/ml in ox Ames at 28\u00b0C for 30 larval retinas or 45 minutes adult retinas. To stop the digestion  the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension  cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30\u00b5m strainer prior to fluorescence activated cell sorting FACS purification. Non transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within 45 minutes post FACS enrichment. Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of 30 000 reads per cell. 10x Chromium three prime v2 platform 10X Genomics  Pleasanton  CA", "GEO Accession:GSM4627220", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP268010", null, "assembly:GRCz10|intentional duplicate", "ZebrafishRGC8.bam", "10X Genomics bam file", 14551197976.0, 148481612.0, "GSM4627220 r1", "0:98", "A:4325239722;C:2863430626;G:2994943270;T:4365215038;N:2369320", 98, null, null, null, 4325239722, 2863430626, 2994943270, 4365215038, 2369320, "SRX8583210", "SRS6874827", "SRA1089100", "GEO", "Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley", 1, 0.87211, null, 0.29067, null, 0.79431, null, 0.49957, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2020-06-19", "Multi-stage", "Multi-stage", "Eye", "Sensory System"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["59864"], "units": {}, "query_ms": 12.11392699769931}