run_metadata: 36668
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 36668 | SRR800037 | SRX257149 | SRS405106 | SRP020008 | PRJNA193544 | Danio rerio strain:Tubingen Epigenomics | PRJNA193544 | Other | 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. | pubmed:23663776 | 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. | Generic sample from Danio rerio | egg RNAseq totalRNARibominus | strain:Tubingen|label:PE: paired end SE: single end|dev stage:egg | egg RNAseq totalRNARibominus | egg RNAseq totalRNARibominus | 7784X1 | 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. | RNA-Seq | TRANSCRIPTOMIC | RT-PCR | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | SRP020008 | 3584440000.0 | 71688800.0 | 7784X1 110323 SN141 0332 A81FDVABXX 8 | 0:50 | A:1013532157;C:812179975;G:992916103;T:765761452;N:50313 | 50 | 1013532157 | 812179975 | 992916103 | 765761452 | 50313 | SRX257149 | SRS405106 | SRA072148 | University of Utah|Brad Cairns Lab | University of Utah | 1 | 0.87304 | 0.12853 | 0.81988 | 0.80407 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | unknown | bulk | unknown | unknown | United States | 2013-04-01 | Undetermined | Embryo | Undetermined | Embryo Imprecise |