{"database": "metadata", "table": "run_metadata", "rows": [[48339, "SRR7762355", "SRX4617972", "SRS3720944", "SRP149356", "PRJNA473799", "Widespread enhancer dememorization and promoter priming during parental to zygotic transition", "GSE114954", "Other", "The epigenome plays critical roles in controlling gene expression and development. However  how the parental epigenomes transit to the zygotic epigenome in early development remains elusive. Here  we show parental to zygotic transition in zebrafish involves extensive erasure of parental epigenetic memory starting by methylating gametic enhancers. Surprisingly  this occurs even prior to fertilization for sperm. Both parental enhancers lose histone marks by the 4 cell stage  and zygotic enhancers are not activated until around zygotic genome activation ZGA. By contrast  many promoters remain hypomethylated and  unexpectedly  acquire de novo histone acetylation as early as at the 4 cell stage. They then resolve into either activated or repressed promoters upon ZGA. Maternal depletion of histone acetyltransferases results in aberrant ZGA and early embryonic lethality. Finally  such reprogramming is largely driven by maternal factors with zygotic products contributing to embryonic enhancer activation. Thus  these data revealed widespread enhancer dememorization and promoter priming during parental to zygotic transition. Overall design: By employing STAR ChIP seq and RNA seq  we systematically examined the genome wide presence of H3K4me3  H3K27ac  H3K27me3 and H3K36me3 in sperm  oocyte  4 cell  256 cell and dome stage embryos.", null, "pubmed:30444999", null, "oocyte II RNA seq", "GSM3359498", null, "tissue:oocyte|developmental stage:stage II|cell type:S phase oocyte|strain:Tu", "oocyte II RNA seq", "RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads.The filtered data were then mapped to the zebrafish reference genome danRer7 by STAR version: STAR 2.5.3a modified with following parameters:   outSAMstrandField intronMotif   outSAMattributes All   outSAMunmapped Within   outSAMattrIHstart 0   outWigStrand Stranded   outFilterMultimapNmax 20   twopassMode Basic. All STAR ChIP seq reads were aligned to the zebrafish reference genome danRer7 using Bowtie2 version 2.2.2 Langmead and Salzberg  2012 with the parameters \u2013t \u2013q \u2013N 1 \u2013L 25. All unmapped reads  non uniquely mapped reads and PCR duplicates were removed. For downstream analysis  the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced RPKM. All STEM seq datasets were mapped to the danRer7 reference genome by Bismark Krueger and Andrews  2011. Reads were trimmed with cutadaptor Martin  2011 using parameters:   minimum length 20   pair filter=any. Alignments were performed with the following parameters:  N 1  X 600   score min L 0  0.6. Multi mapped reads and PCR duplicates were removed. bismark methylation extractor was used to calculate the DNA methylation level Genome build: danRer7 Supplementary files format and content: Bigwig for ChIP seq and RNA seq tracks  gene expression table for RNA seq data", "oocyte", "The ovaries of adult female were isolated and transferred into specific buffer 5.4 mM KCl  136.8 mM NaCl  4.2 mM NaHCO3  0.44 mM KH2PO4  0.25 mM Na2HPO4  and 0.5% wt/vol BSA. Then stage I V oocytes were separated from the ovary with tweezers under microscope according to their morphology  and the surrounding follicle cells were detached gently as much as possible.", "Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN  74104 as recommended protocols 5 ug RNA was DNase I Fermentas  Cat # EN0521 treated at 37C for 1 h. RNA was then purified using AMPure beads. Poly A tailed mRNA was collected using DynabeadsTM mRNA purification kit Invitrogen  Cat # 61006. Purified RNA was fragmented with RNA Frag. Buffer NEB  Cat # E6186A at 95C for 5 min. Reaction was stopped and RNA was purified by AMPure beads. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers Invitrogen  Cat # 18080 051. Second strand cDNA was synthesized with second strand synthesis buffer Invitrogen  Cat # 10812014  MgCl2  DTT  dNTP  dUTP  RNase H Fermentas  Cat # EN0202  E. coli DNA ligase NEB  Cat # M0205S and DNA polymerase I NEB  Cat # M0209S. DNA was purified post 2 hrs incubation on thermomixer at 16C. Synthesized cDNA was subjected to library preparation. DNA was end repaired  adenylated  and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG AMPErase  Cat # N808 0096 at 37C for 1 hour followed by DNA amplification using Phusion HF DNA polymerase NEB  Cat # M0530L. The amplified DNA was size selected using AMPure Beads for 200 500 bp DNA fragments.", "The wild type Tu female strain were raised as standard protocol.", "developmental stage:stage II|cell type:S phase oocyte|strain:Tu", "GSM3359498", "GSM3359498: oocyte II RNA seq; Danio rerio; RNA Seq", "GSM3359498", null, "1", "Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN  74104 as recommended protocols 5 ug RNA was DNase I Fermentas  Cat # EN0521 treated at 37C for 1 h. RNA was then purified using AMPure beads. Poly A tailed mRNA was collected using DynabeadsTM mRNA purification kit Invitrogen  Cat # 61006. Purified RNA was fragmented with RNA Frag. Buffer NEB  Cat # E6186A at 95C for 5 min. Reaction was stopped and RNA was purified by AMPure beads. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers Invitrogen  Cat # 18080 051. Second strand cDNA was synthesized with second strand synthesis buffer Invitrogen  Cat # 10812014  MgCl2  DTT  dNTP  dUTP  RNase H Fermentas  Cat # EN0202  E. coli DNA ligase NEB  Cat # M0205S and DNA polymerase I NEB  Cat # M0209S. DNA was purified post 2 hrs incubation on thermomixer at 16C. Synthesized cDNA was subjected to library preparation. DNA was end repaired  adenylated  and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG AMPErase  Cat # N808 0096 at 37C for 1 hour followed by DNA amplification using Phusion HF DNA polymerase NEB  Cat # M0530L. The amplified DNA was size selected using AMPure Beads for 200 500 bp DNA fragments.", "GEO Accession:GSM3359498", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP149356", null, null, "oocyte_II_RNA_seq_r1.fq.gz", "fastq", 636518379.0, 12990171.0, "GSM3359498 r1", "0:49 1:0", "A:160017029;C:153897668;G:159821522;T:162670200;N:111960", 49, 0, null, null, 160017029, 153897668, 159821522, 162670200, 111960, "SRX4617972", "SRS3720944", "SRA712563", "GEO", "Tsinghua University", 1, 0.9326, null, 0.0241, null, 0.74073, null, 0.47431, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "China", "2018-08-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["48339"], "units": {}, "query_ms": 10.015006999310572}