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Sample GSM2101161 Query DataSets for GSM2101161
Status Public on Sep 15, 2016
Title ChIP-Seq Maternal pronucleus of PN3 zygote K4Me3
Sample type SRA
 
Source name Preimplantation embryo
Organism Mus musculus
Characteristics strain: C57BL/6N
tissue: Preimplantation embryo
chip antibody: custom-made H3K4Me3 antibody (Abmart)
Treatment protocol Zygotes at PN3-4 stage were collected from superovulated C57BL/6N female that mated to BDA/2N males. Female pronuclei were collected using a piezo-drill micromanipulator and the residuals that contain male pronuclei were then treated by pronase to remove the zona pellucida. After that, these samples were incubated in lysis buffer for ChIP-seq.
Extracted molecule genomic DNA
Extraction protocol Female pronuclei were collected using a piezo-drill micromanipulator and the residuals that contain male pronuclei were then treated by pronase to remove the zona pellucida. After that, these samples were incubated in lysis buffer for ChIP-seq.
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 Mar 29, 2016
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
BioSample SAMN04589803
SRA SRX1668471

Supplementary file Size Download File type/resource
GSM2101161_Maternal_pronucleus_K4me3.bed.gz 889.7 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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