run_metadata: 29104
This data as json
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| 29104 | SRR27010852 | SRX22703632 | SRS19696107 | SRP475451 | PRJNA1047750 | Differential expression in Muller glia of injured zebrafish in a mych / context | GSE249115 | 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 mych / Muller glia from injured mych / fish at 2dpi. Of interest are the WT injury responsive genes and which injury responsive genes in the WT are differentially expressed in the mych / fish. | parent bioproject:PRJNA1047494 | pubmed:38984586 | Muller glia from uninjured WT retinas rep3 [5803 ML 3] | GSM7926864 | source name:WT Muller glia uninjured retina|tissue:WT Muller glia uninjured retina|genotype:WT|treatment:n1|geo loc name:missing|collection date:missing | Muller glia from uninjured WT retinas rep3 [5803 ML 3] | 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: RS10 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample | WT Muller glia uninjured 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 uninjured retina|genotype:WT|treatment:n1 | GSM7926864 | GSM7926864: Muller glia from uninjured WT retinas rep3 [5803 ML 3]; Danio rerio; RNA Seq | GSM7926864 r1 | GSM7926864 | 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 | SRP475451 | loader:fastq load.py | 5803-ML-3_CCTTATGG-GCACGCTT_S216_R2_001.fastq.gz 5803-ML-3_CCTTATGG-GCACGCTT_S216_R1_001.fastq.gz | fastq fastq | 44024352302.0 | 145776001.0 | GSM7926864 r1 | 0:151 1:151 | A:12035679681;C:9067037632;G:11325935498;T:11595599635;N:99856 | 151 | 151 | 12035679681 | 9067037632 | 11325935498 | 11595599635 | 99856 | SRX22703632 | SRS19696107 | SRA1761648 | University of Michigan | University of Michigan | 2 | 0.83165 | 0.79093 | 0.139 | 0.11939 | 0.73539 | 0.74148 | 0.52839 | 0.52569 | 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 |