run_metadata: 34476
This data as json
| 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 |
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| 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. | adult zebrafish retinal ganglion cells 1 xxx post injury fish set #2 | GSM8691387 | 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 Kölsch 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’s 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’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ 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. | 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. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP552478 | 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 | 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 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2024-12-18 | Adult | Adult | Eye | Sensory System |