run_metadata: 29103
This data as json
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| 29103 | SRR27010851 | SRX22703633 | SRS19696108 | 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 WT retinas 2 xxx post injury dpi rep1 [5803 ML 4] | GSM7926865 | source name:WT Muller glia injured retina|tissue:WT Muller glia injured retina|genotype:WT|treatment:injured|geo loc name:missing|collection date:missing | Muller glia from WT retinas 2 xxx post injury dpi rep1 [5803 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: RS10 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:injured | GSM7926865 | GSM7926865: Muller glia from WT retinas 2 xxx post injury dpi rep1 [5803 ML 4]; Danio rerio; RNA Seq | GSM7926865 r1 | GSM7926865 | 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-4_TTACACAC-AACTCCGA_S217_R1_001.fastq.gz 5803-ML-4_TTACACAC-AACTCCGA_S217_R2_001.fastq.gz | fastq fastq | 35641811084.0 | 118019242.0 | GSM7926865 r1 | 0:151 1:151 | A:9509123801;C:7547711759;G:9554254572;T:9030640032;N:80920 | 151 | 151 | 9509123801 | 7547711759 | 9554254572 | 9030640032 | 80920 | SRX22703633 | SRS19696108 | SRA1761648 | University of Michigan | University of Michigan | 2 | 0.84325 | 0.81491 | 0.09102 | 0.08021 | 0.71936 | 0.72368 | 0.52206 | 0.51772 | 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 |