run_metadata: 29093
This data as json
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| 29093 | SRR27010840 | SRX22703627 | SRS19696102 | SRP475450 | PRJNA1047749 | Differential expression in Muller glia of injured zebrafish in a mycb / context | GSE249116 | Transcriptome Analysis | This experiment studies retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas injured WT Muller glia from injured WT retina at 2 xxx post injury dpi and injured mycb / Muller glia from injured mycb / fish at 2dpi. | parent bioproject:PRJNA1047494 | pubmed:38984586 | Muller glia from mycb / retinas 2 xxx post injury dpi rep1 [7131 ML 7] [7131 ML 7] | GSM7926875 | source name:mycb / Muller glia injured retina|tissue:mycb / Muller glia injured retina|genotype:mycb / |treatment:injured|geo loc name:missing|collection date:missing | Muller glia from mycb / retinas 2 xxx post injury dpi rep1 [7131 ML 7] [7131 ML 7] | University of Michigan Bioinformatics Core RNA seq pipeline "Watermelon" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS11 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample | mycb / Muller glia injured retina | Needle poke injury to retina. | Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions. | tissue:mycb / Muller glia injured retina|genotype:mycb / |treatment:injured | GSM7926875 | GSM7926875: Muller glia from mycb / retinas 2 xxx post injury dpi rep1 [7131 ML 7] [7131 ML 7]; Danio rerio; RNA Seq | GSM7926875 r1 | GSM7926875 | 1 | Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP475450 | loader:fastq load.py | 7131-ML-7_TTACGGAC-ATTGGCCA_S73_R1_001.fastq.gz 7131-ML-7_TTACGGAC-ATTGGCCA_S73_R2_001.fastq.gz | fastq fastq | 27084816546.0 | 89684823.0 | GSM7926875 r1 | 0:151 1:151 | A:7489987820;C:5729672678;G:6569226079;T:7295655071;N:274898 | 151 | 151 | 7489987820 | 5729672678 | 6569226079 | 7295655071 | 274898 | SRX22703627 | SRS19696102 | SRA1761650 | University of Michigan | University of Michigan | 2 | 0.8887 | 0.84473 | 0.12952 | 0.10995 | 0.73338 | 0.74211 | 0.54826 | 0.56906 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2023-12-01 | Undetermined | Undetermined | Eye | Sensory System |