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Sample GSM2041067 Query DataSets for GSM2041067
Status Public on Sep 15, 2016
Title ChIP-Seq growing oocyte 7days K27Me3
Sample type SRA
Source name Growing oocyte
Organism Mus musculus
Characteristics strain: C57BL/6N
tissue/cell type: Growing oocyte
chip antibody: H3K27Me3
chip antibody vendor: Diagenode
chip antibody cat. #: C15410069; pAb-069-050
Treatment protocol Follicles were isolated from 10-day old C57BL/6 mice by mechanical dissection using a 26 gauge needle, followed by the digestion with 4 mg/ml of collagenase I and 0.02 mg/ml of DNase I in L15 medium for 30 min at 37°C. To remove the granulosa cells, the dissociated oocyte-granulosa cells complexes were transferred into PBS (Ca2+, Mg2+-free) containing 1 mg/ml of collagenase I and were digested for 20 min. Oocytes were then incubated in lysis buffer after removing the zona pellucida by pronase treatment.
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
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
BioSample SAMN04419956
SRA SRX1533816

Supplementary file Size Download File type/resource
GSM2041067_Growing_oocyte_14days_k27me3_broadpeak.bed.gz 209.3 Kb (ftp)(http) BED
GSM2041067_Growing_oocyte_7days_k27me3.bed.gz 71.5 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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