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Sample GSM1845283 Query DataSets for GSM1845283
Status Public on Sep 15, 2016
Title ChIP-Seq PN5 zygote histone H3
Sample type SRA
 
Source name Preimplantation embryo
Organism Mus musculus
Characteristics strain: C57BL/6N x PWK
developmental stage: Preimplantation embryo
chip antibody: custom-made H3K4Me3 antibody (Abmart)
Treatment protocol Embryos were collected from C57BL/6N mice induced to superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours apart and mated to PWK males. Each set of embryos at a particular stage was flushed from the reproductive tract at defined time periods after hCG administration: 20h (MII oocyte), 27-28h (PN5 zygote), 30h (early 2-cell), 43h (late 2-cell), 54-56 h (4-cell), 68-70 h (8-cell) and 92-94 h (blastocysts) in Hepes-buffered CZB medium. The zona pellucida of embryos selected by cell number or morphology was gently removed by treatment of 10 IU/ml pronase (Sigma P8811) for several minutes. The embryos were then manually picked and treated with the lysis buffer for STAR ChIP-seq or Smart-seq2.
Extracted molecule genomic DNA
Extraction protocol After removing the zona pellucida, embryonic cells were washed with PBS and incubated in lysis buffer.
ChIP-Seq libraries were prepared using TELP developed by PengXu et al. with slightly modification
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Data processing Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
RNA-Seq reads were aligned to the mm9 genome assembly using Tophat version 2.0.11, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: The bed files include RPKM values in 100bp bins for each ChIP-seq sample. Bed files labeled maternal or paternal contain RPKM values for two parental alleles, allelic reads were normalized to total reads number. Tab-delimited text files include FPKM values RNA-seq sample.
 
Submission date Aug 06, 2015
Last update date May 15, 2019
Contact name Bingjie Zhang
Organization name Tsinghua University
Street address 30 Shuangqing Rd
City Beijing
State/province Beijing
ZIP/Postal code 100190
Country China
 
Platform ID GPL18480
Series (1)
GSE71434 Allelic reprogramming of the histone modification H3K4me3 in early mammalian development
Relations
SRA SRX1134820
BioSample SAMN03979652

Supplementary file Size Download File type/resource
GSM1845283_PN5_zygote_histone_H3.bed.gz 173.7 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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