run_metadata: 29098
This data as json
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| 29098 | SRR27010846 | SRX22703638 | SRS19696113 | 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 mych / retinas 2 xxx post injury dpi rep3 [5803 ML 10] | GSM7926870 | source name:mych / Muller glia injured retina|tissue:mych / Muller glia injured retina|genotype:mych / |treatment:injured|geo loc name:missing|collection date:missing | Muller glia from mych / retinas 2 xxx post injury dpi rep3 [5803 ML 10] | 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 | mych / 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:mych / Muller glia injured retina|genotype:mych / |treatment:injured | GSM7926870 | GSM7926870: Muller glia from mych / retinas 2 xxx post injury dpi rep3 [5803 ML 10]; Danio rerio; RNA Seq | GSM7926870 r1 | GSM7926870 | 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-10_AACAACGG-TTACACCT_S222_R1_001.fastq.gz 5803-ML-10_AACAACGG-TTACACCT_S222_R2_001.fastq.gz | fastq fastq | 33066899590.0 | 109493045.0 | GSM7926870 r1 | 0:151 1:151 | A:9045925528;C:7063243555;G:8277253275;T:8680404068;N:73164 | 151 | 151 | 9045925528 | 7063243555 | 8277253275 | 8680404068 | 73164 | SRX22703638 | SRS19696113 | SRA1761648 | University of Michigan | University of Michigan | 2 | 0.87174 | 0.82563 | 0.12217 | 0.10466 | 0.7052 | 0.71311 | 0.50335 | 0.51416 | 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 |