run_metadata: 34447
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 34447 | SRR31768861 | SRX27130600 | SRS23587604 | SRP552464 | PRJNA1200121 | Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq] | GSE284728 | 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: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1 5 and 7 xxx post injury dpi and three from uninjured tissue on the same days. | adult zebrafish retinal ganglion cells day 7 uninjured fish set #3 | GSM8691385 | 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:uninjured|time:day 7|geo loc name:missing|collection date:missing | adult zebrafish retinal ganglion cells day 7 uninjured fish set #3 | Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups post genes with TPM=0 in one or more replicates were excluded. DEGs from 1 5 and 7 dpi time points were identified using the following filter: the maximum of the average group RPKM value >1.5 absolute fold change >1.5 FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample | 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 5 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc. | 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:uninjured|time:day 7 | GSM8691385 | GSM8691385: adult zebrafish retinal ganglion cells day 7 uninjured fish set #3; Danio rerio; RNA Seq | GSM8691385 r1 | GSM8691385 | 1 | 1 5 and 7 xxx post injury dpi the retina were harvested cells dissociated using papain digestion and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 2000 | SRP552464 | 7DPI_uninjured_03_S30_R1_001.fastq.gz 7DPI_uninjured_03_S30_R2_001.fastq.gz | fastq fastq | 5698047024.0 | 29362783.0 | GSM8691385 r1 | 0:97.02 1:97.03 | A:1667059209;C:1124020328;G:1186053751;T:1719272359;N:1641377 | 97 | 97 | 1667059209 | 1124020328 | 1186053751 | 1719272359 | 1641377 | SRX27130600 | SRS23587604 | SRA2037426 | 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 | B | B | biological fallback assumption | illumina | nextseq_v2 | unknown | cdna_unspecified | nextera | bulk | bulk | bulk | United States | 2024-12-18 | Adult | Adult | Eye | Sensory System |