{"database": "metadata", "table": "run_metadata", "rows": [[76696, "SRR25253553", "SRX20999596", "SRS18272869", "SRP449239", "PRJNA994180", "Evolution of neuronal cell classes and types in the vertebrate retina [Zebrafish]", "GSE237214", "Transcriptome Analysis", "The basic plan of the retina is conserved across vertebrates  yet species differ profoundly in their visual needs Baden et al.  2020. One might expect that retinal cell types evolved to accommodate these varied needs  but this has not been systematically studied. Here  we generated and integrated single cell transcriptomic atlases of the retina from 17 species: humans  two non human primates  four rodents  three ungulates  opossum  ferret  tree shrew  a teleost fish  a bird  a reptile and a lamprey. Molecular conservation of the six retinal cell classes photoreceptors  horizontal cells  bipolar cells  amacrine cells  retinal ganglion cells [RGCs] and M\u00fcller glia is striking  with transcriptomic differences across species correlated with evolutionary distance. Major subclasses are also conserved  whereas variation among types within classes or subclasses is more pronounced. However  an integrative analysis revealed that numerous types are shared across species based on conserved gene expression programs that likely trace back to the common ancestor of jawed vertebrates. The degree of variation among types increases from the outer retina photoreceptors to the inner retina RGCs  suggesting that evolution acts preferentially to shape the retinal output. Finally  we identified mammalian orthologs of midget RGCs  which comprise >80% of RGCs in the human retina  subserve high acuity vision  and were believed to be primate specific Berson  2008; in contrast  the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus  which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations  but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved  thereby facilitating high visual acuity and increased cortical processing of visual information. Overall design: Single cell RNA seq was performed on cells isolated from fresh retina. Fluorescence activated cell sorting was used to collect Calcein blueCB positive live cells. For some collections  CB+ cells were further seprated using CD90/THY1 and/or CD73 expression as an strategy to enrich for RGCs and/or to deplete phototreceptors  respectively Please note that he enrichment strategy was not effective for some species/samples. Approximately 8000 cells were recovered from each sample  and each cell was sequenced to a depth of 40000 reads.", "parent bioproject:PRJNA994164", "pubmed:38092908", null, "Zebrafish BC3", "GSM7596937", null, "source name:Retina|tissue:Retina|cell type:Retinal neurons|geo loc name:missing|collection date:missing", "Zebrafish BC3", "We used cellranger v7.0  10X Genomics to align the sc  and snRNA seq datasets  following manufacturer\u2019s instructions. For each species  sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map .bam files. Assembly: Zv82 Supplementary files format and content: To include both exonic and intronic reads in the quantification of gene expression for each sample  regardless of cellular or nuclear origin  we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices GEMs; genes x cells for each sample  corresponding to \u201cspliced\u201d and \u201cunspliced\u201d reads. The two GEMs were summed element by element to obtain \u201ctotal\u201d GEM for each sample. Supplementary files format and content: GEMs from different sample runs were combined column wise concatenated to yield a full species\u2019 GEM.", "Retina", "None", "Retinas were dissected in Ames solution Sigma Aldrich; equilibrated with 95% O2/5% CO2 for all use immediately following enucleation. They were dissociated in papain  followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors. Single cell libraries were generated using the Chromium 3\u2019 V3 platform 10X Genomics  Pleasanton  CA according to the manufacturer\u2019s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full length cDNA; this was followed by amplification  enzymatic fragmentation  and 5\u2019 adaptor and sample index attachment to yield the final libraries. Single cell RNA sequecning 10X Genomics", null, "tissue:Retina|cell type:Retinal neurons", "GSM7596937", "GSM7596937: Zebrafish BC3; Danio rerio; RNA Seq", "GSM7596937 r1", "GSM7596937", "1", "Retinas were dissected in Ames solution Sigma Aldrich; equilibrated with 95% O2/5% CO2 for all use immediately following enucleation. They were dissociated in papain  followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors. Single cell libraries were generated using the Chromium three prime V3 platform 10X Genomics  Pleasanton  CA according to the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full length cDNA; this was followed by amplification  enzymatic fragmentation  and five prime adaptor and sample index attachment to yield the final libraries. Single cell RNA sequecning 10X Genomics", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP449239", null, "intentional duplicate", "ZfishBC3.bam", "10X Genomics bam file", 4133686256.0, 42180472.0, "GSM7596937 r1", "0:98", "A:1223733383;C:788484354;G:823319620;T:1297264565;N:884334", 98, null, null, null, 1223733383, 788484354, 823319620, 1297264565, 884334, "SRX20999596", "SRS18272869", "SRA1672086", "Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley", "Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley", 1, 0.85846, null, 0.22015, null, 0.81716, null, 0.48798, null, 98, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-07-12", "Undetermined", "Undetermined", "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": ["76696"], "units": {}, "query_ms": 8.645820009405725}