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SRX257155: sphere_RNAseq_5azaCyD_treatment
1 ILLUMINA (Illumina HiSeq 2000) run: 51.9M spots, 2.6G bases, 1.7Gb downloads

Design: 1nl of 1mM 5-AzadCyD was injected into 1-cell stage embryos, which were then incubated in 100uM 5-AzadCyD until sphere stage and collected. Embryos injected with water served as control. Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit (Cat # 80004), ribosomal RNA was depleted using RiboMinus kit (A10837-08, Eukaryote Kit) followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.
Submitted by: UNIVERSITY OF UTAH
Study: Danio rerio strain:Tubingen Epigenomics
show Abstracthide Abstract
Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation (ZGA). To better understand, we determined DNAme profiles of zebrafish gametes, multiple embryo stages flanking ZGA, and somatic muscle - and compared them to gene activity and histone modifications. First, sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly, in the oocyte many genes important for germline functions (ie. piwil1) or early development (ie. hox genes) are DNA methylated. Remarkably, these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm, even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore, this cohort constitutes the genes/loci that acquire DNAme during development (ie. ZGA to muscle). Finally, DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA, preventing their precocious expression. Thus, zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.
Sample: Generic sample from Danio rerio
SAMN01991181 • SRS405709 • All experiments • All runs
Organism: Danio rerio
Library:
Name: 9323X1
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: RT-PCR
Layout: SINGLE
Spot descriptor:
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Runs: 1 run, 51.9M spots, 2.6G bases, 1.7Gb
Run# of Spots# of BasesSizePublished
SRR80004651,913,0912.6G1.7Gb2013-05-07

ID:
359238

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