run_metadata: 69652
This data as json
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| 69652 | SRR19084414 | SRX15154222 | SRS12896743 | SRP373610 | PRJNA835051 | The regeneration responsive careg element monitors activation of Müller glia post MNU induced damage in the zebrafish retina | GSE202212 | Transcriptome Analysis | We found that the zebrafish non coding element careg which is induced in regenerating fins and heart also participates in retina regeneration. Its activation persisted mostly in Müller glia from the onset to the termination of retina restoration. To assess the involvement of the careg:EGFP reporter during retina regeneration we used a chemical injury model with MNU treatment. To identify the molecular profile of these cells we performed a single cell RNA sequencing scRNA seq experiment of retinas dissected from adult careg:EGFP zebrafish at 3 7 and 10 dpMNU. Our control retinas were dissected from fish at 3 days post treatment with heat inactivated MNU Overall design: Adult careg:EGFP transgenic zebrafish retinas post MNU induced injury were isolated for scRNA sequencing | pubmed:37138703 | uninjured 1 | GSM6106352 | source name:retina|tissue:adult retina|strain:Tgcareg:EGFP|treatment:1h treatment with heat inactivated MNU|geo loc name:missing|collection date:missing | uninjured 1 | Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.2.0 The GFP transcript sequence was added manually to the reference assembly. Further processing was performed using Seurat v4 in R. Assembly: GRCz11 Supplementary files format and content: gene barcode expression matrix | retina | Retina was extracted from eyeball and retina cells were dissociated in liberase 2.5 mg/mL. Libraries for scRNA seq were prepared using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 10X Genomics. | tissue:adult retina|strain:Tgcareg:EGFP|treatment:1h treatment with heat inactivated MNU | GSM6106352 | GSM6106352: uninjured 1; Danio rerio; RNA Seq | GSM6106352 r1 | GSM6106352 | 1 | Retina was extracted from eyeball and retina cells were dissociated in liberase 2.5 mg/mL. Libraries for scRNA seq were prepared using the Chromium Single Cell three prime Library and Gel Bead Kit v3 10X Genomics. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP373610 | assembly:GRCz11|intentional duplicate|dangling references:treat as unmapped | ctrl1_possorted_genome_bam.bam | 10X Genomics bam file | 43888459732.0 | 485067105.0 | GSM6106352 r1 | 0:90.48 | A:13055406117;C:8931800171;G:9711907132;T:12176465725;N:12880587 | 90 | 13055406117 | 8931800171 | 9711907132 | 12176465725 | 12880587 | SRX15154222 | SRS12896743 | SRA1420445 | University of Fribourg | University of Fribourg | 1 | 0.88385 | 0.35485 | 0.8089 | 0.55076 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Switzerland | 2022-05-04 | Adult | Adult | Eye | Sensory System |