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Sample GSM1845262 Query DataSets for GSM1845262
Status Public on Sep 15, 2016
Title ChIP-Seq MII oocyte K4Me3 rep1
Sample type SRA
Source name MII oocyte
Organism Mus musculus
Characteristics strain: C57BL/6N
developmental stage: MII oocyte
chip antibody: custom-made H3K4Me3 antibody (Abmart)
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. with slightly modification
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
Description processed data files: MII_oocyte_K4me3_broadpeak.bed.gz
Data processing Basecalls performed using CASAVA version 1.8
ChIP-seq peaks were called using MACS2 with the parameters --broad --nomodel --nolambda and noisy peaks with very weak signals (summed RPKM < 30) were removed.
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 counted by the number of reads falling into 100bp bin in the genome. Tab-delimited bed files include RPKM values for each sample. The peak files included regions of all peaks called in each 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
SRA SRX1134799
BioSample SAMN03979631

Supplementary file Size Download File type/resource
GSM1845262_MII_oocyte_K4me3_rep1.bed.gz 54.9 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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