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"Embryo Imprecise", "All anatomical structures"], [36663, "SRR800049", "SRX257156", "SRS405710", "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.", null, "pubmed:23663776", "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.", "Generic sample from Danio rerio", "sphere RNAseq 5azaCyD control", null, "strain:Tubingen|label:PE: paired end  SE: single end|development stage:sphere", null, null, null, null, null, null, null, null, "sphere RNAseq 5azaCyD control", "sphere RNAseq 5azaCyD control", "9323X2", "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.", null, null, "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", null, null, "sphere_RNAseq_5azaCyD_control_SE_9323X2_120628_SN141_0513_AD12CFACXX_4.txt.gz", "Illumina native", 2563410950.0, 51268219.0, "9323X2 120628 SN141 0513 AD12CFACXX 4", "0:50", "A:663337120;C:603101927;G:752336300;T:542924123;N:1711480", 50, null, null, null, 663337120, 603101927, 752336300, 542924123, 1711480, "SRX257156", "SRS405710", "SRA072148", "University of Utah|Brad Cairns Lab", "University of Utah", 1, 0.65713, null, 0.09976, null, 0.81677, null, 0.81063, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-05-07", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36664, "SRR800046", "SRX257155", "SRS405709", "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.", null, "pubmed:23663776", "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.", "Generic sample from Danio rerio", "sphere RNAseq 5azaCyD treatment", null, "strain:Tubingen|label:PE: paired end  SE: single end|development stage:sphere", null, null, null, null, null, null, null, null, "sphere RNAseq 5azaCyD treatment", "sphere RNAseq 5azaCyD treatment", "9323X1", "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. 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