run_metadata: 29095
This data as json
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| 29095 | SRR27010842 | SRX22703625 | SRS19696100 | 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 WT retinas 2 xxx post injury dpi rep1 [7131 ML 4] [7131 ML 4] | GSM7926873 | source name:WT Muller glia injured retina|tissue:WT Muller glia injured retina|genotype:WT|treatment:n1|geo loc name:missing|collection date:missing | Muller glia from WT retinas 2 xxx post injury dpi rep1 [7131 ML 4] [7131 ML 4] | 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 | WT 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:WT Muller glia injured retina|genotype:WT|treatment:n1 | GSM7926873 | GSM7926873: Muller glia from WT retinas 2 xxx post injury dpi rep1 [7131 ML 4] [7131 ML 4]; Danio rerio; RNA Seq | GSM7926873 r1 | GSM7926873 | 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-4_TTAACGGC-CTCCGTCT_S70_R1_001.fastq.gz 7131-ML-4_TTAACGGC-CTCCGTCT_S70_R2_001.fastq.gz | fastq fastq | 36567606580.0 | 121084790.0 | GSM7926873 r1 | 0:151 1:151 | A:9477563071;C:8136361552;G:9699876329;T:9253435137;N:370491 | 151 | 151 | 9477563071 | 8136361552 | 9699876329 | 9253435137 | 370491 | SRX22703625 | SRS19696100 | SRA1761650 | University of Michigan | University of Michigan | 2 | 0.85059 | 0.82538 | 0.08689 | 0.07693 | 0.73574 | 0.74371 | 0.54735 | 0.54664 | 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 |