run_metadata: 40756
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 40756 | SRR5398212 | SRX2692999 | SRS2089612 | 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 36hpf | GSM2560112 | source name:whole eye tissue|strain:TL|genotype/variation:sibling control|tissue:dissected eyes|age:36 hpf | sibling at 36hpf | base calling demultiplexing done at University of Pittsburgh Genomic Research Core fastq files quality checked using FastQC mapped using CLC Genomics Grid Worker 7.5.1 gene counting and differentially expressed genes identified using CLC Genomics Grid Worker 7.5.1 Genome build: GRCz10 Supplementary files format and content: Tet23 36hpf GE all.xlsx | 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:36 hpf | GSM2560112 | GSM2560112: sibling at 36hpf; Danio rerio; RNA Seq | GSM2560112 | 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:GSM2560112 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP073099 | Tet23_WT_S2B_L004_R1_001.fastq.gz Tet23_WT_S2B_L004_R2_001.fastq.gz | fastq fastq | 2527779000.0 | 16851860.0 | GSM2560112 r8 | 0:75 1:75 | A:667174371;C:572028335;G:630346069;T:658063231;N:166994 | 75 | 75 | 667174371 | 572028335 | 630346069 | 658063231 | 166994 | SRX2692999 | SRS2089612 | SRA409011 | GEO | Gross, Ophthalmology, University of Pittsburgh | 2 | 0.95204 | 0.95131 | 0.08427 | 0.08315 | 0.7321 | 0.73693 | 0.49314 | 0.48924 | 75 | 75 | B | B | biological fallback assumption | illumina | nextseq | unknown | poly_a | nebnext | bulk | unknown | unknown | United States | 2017-03-30 | Pharyngula | Embryo | Eye | Sensory System |