run_metadata: 40765
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 40765 | SRR3355805 | SRX1689713 | SRS1384139 | SRP073099 | PRJNA318016 | Tet mediated DNA hydroxymethylation regulates retinal neurogenesis in zebrafish via cell extrinsic signaling pathways | GSE80134 | Transcriptome Analysis | Using zebrafish tet2 / ;tet3 / mutants we identify functions for Tet enzymes and 5 hydroxymethylcytosine 5hmC in regulating gene expression and cell type specific differentiation during retinal development. Overall design: RNAseq from tet2 / ;tet3 / mutant and sibling embryonic eye tissues dissected at 72hpf and 36hpf. | pubmed:28926578 | sibling at 72hpf | GSM2113394 | source name:whole eye tissue|strain:TL|genotype/variation:sibling control|tissue:dissected eyes|age:72 hpf | sibling at 72hpf | base calling demultiplexing done at the Genome Sequenicng and Analysis Facility UT Austin fastq files quality checked using FastQC mapped using TopHat with annotated spliced junction gene counting and differentially expressed genes identified using Tuxedo Suite Trapnell et al. 2012 Genome build: GRCz10 | whole eye tissue | none | whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. | zebrafish embryos raised under standard condition | strain:TL|genotype/variation:sibling control|tissue:dissected eyes|age:72 hpf | GSM2113394 | GSM2113394: sibling at 72hpf; Danio rerio; RNA Seq | GSM2113394 | 1 | whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. | GEO Accession:GSM2113394 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP073099 | tet23_WT_GTCCGC_L001_R1_001.fastq.gz tet23_WT_GTCCGC_L001_R2_001.fastq.gz | fastq fastq | 2760449832.0 | 10954166.0 | GSM2113394 r1 | 0:126 1:126 | A:749168042;C:630997286;G:640050974;T:738938277;N:1295253 | 126 | 126 | 749168042 | 630997286 | 640050974 | 738938277 | 1295253 | SRX1689713 | SRS1384139 | SRA409011 | GEO | Gross, Ophthalmology, University of Pittsburgh | 2 | 0.94057 | 0.93996 | 0.11845 | 0.11794 | 0.70088 | 0.70193 | 0.45873 | 0.45468 | 126 | 126 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | nebnext | bulk | unknown | unknown | United States | 2016-04-11 | Larval | Larval | Eye | Sensory System |