{"database": "metadata", "table": "run_metadata", "rows": [[34476, "SRR31769128", "SRX27130819", "SRS23587806", "SRP552478", "PRJNA1200128", "Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq]", "GSE284729", "Transcriptome Analysis", "Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.", null, null, null, "adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #2", "GSM8691387", null, "source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing", "adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #2", "The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by K\u00f6lsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat\u2019s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix", "retina", "Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.", "1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer\u2019s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.", "isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.", "tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury", "GSM8691387", "GSM8691387: adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #2; Danio rerio; RNA Seq", "GSM8691387 r1", "GSM8691387", "1", "1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "Injured-1DPI-2_GRO2553A8_S12_L001_R1_001.fastq.gz Injured-1DPI-2_GRO2553A8_S12_L001_R2_001.fastq.gz", "fastq fastq", 91792694538.0, 777904191.0, "GSM8691387 r1", "0:28 1:90", "A:25675360853;C:20502226198;G:22024452743;T:23588401816;N:2252928", 28, 90, null, null, 25675360853, 20502226198, 22024452743, 23588401816, 2252928, "SRX27130819", "SRS23587806", "SRA2037459", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", "Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-18", "Adult", "Adult", "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": ["34476"], "units": {}, "query_ms": 10.190143002546392}