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Sample GSM2041070 Query DataSets for GSM2041070
Status Public on Sep 15, 2016
Title ChIP-Seq MII oocyte K27Me3 rep1
Sample type SRA
 
Source name MII oocyte
Organism Mus musculus
Characteristics strain: C57BL/6N
tissue/cell type: MII oocyte
chip antibody: H3K27Me3
chip antibody vendor: Diagenode
chip antibody cat. #: C15410069; pAb-069-050
Treatment protocol Collection of MII oocytes from superovulated C57BL/6N mice was performed 20h after hCG injection.
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. (PMID: 25223787) with slightly modification.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Description processed data file: MII_oocyte_k27me3.bed.gz
MII_oocyte_k27me3_broadpeak.bed.gz
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 Jan 18, 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)
GSE76687 Resetting epigenetic memory by reprogramming of histone modifications in mammals
Relations
BioSample SAMN04419959
SRA SRX1533819

Supplementary file Size Download File type/resource
GSM2041070_MII_oocyte_k27me3_rep1.bed.gz 30.9 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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