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Sample GSM1845259 Query DataSets for GSM1845259
Status Public on Sep 15, 2016
Title ChIP-Seq growing oocyte 10days K4Me3
Sample type SRA
 
Source name Growing oocyte
Organism Mus musculus
Characteristics strain: C57BL/6N
developmental stage: Growing oocyte
chip antibody: custom-made H3K4Me3 antibody (Abmart)
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. 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 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
Relations
SRA SRX1134796
BioSample SAMN03979628

Supplementary file Size Download File type/resource
GSM1845259_growing_oocyte_10days_K4me3.bed.gz 49.6 Mb (ftp)(http) BED
GSM1845259_growing_oocyte_10days_K4me3_broadpeak.bed.gz 368.5 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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