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Sample GSM4832691 Query DataSets for GSM4832691
Status Public on Feb 04, 2021
Title WGBS-GV-WT1
Sample type SRA
 
Source name WT mouse GV oocytes
Organism Mus musculus
Characteristics stain: C57BL/6
Treatment protocol 4 week mouse treated by PMSG 44 h
Growth protocol in vivo
Extracted molecule genomic DNA
Extraction protocol GV oocytes were collected from 3-week old WT and Cxxc1fl/fl;Gdf9-Cre mice. For each sample, 200 oocytes were picked into cell lysis buffer using mouth pipet. Then we performed scBS-seq protocol with slight modification.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2500
 
Data processing ChIP-seq data analysis.ChIP-seq reads were trimmed to 50 bp and aligned to the mouse genome build mm9 using bowtie2 (v2.3.4.1) with default parameters. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. H3K4me3 peaks were called using MACS2 (v 2.1.1.20160309) with the parameters “--nomodel --nolambda --broad -B --SPMR -g mm” and signal tracks for each sample were generated with “wigToBigWig” from UCSC.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig
WGBS data analysis. Raw reads were trimmed using TrimGalore (v 0.4.4) with default parameters. Then the reads were mapped to converted mm9 reference using bismark (v0.19.0) with parameters “--bowtie2 --non_directional”. PCR duplicates were removed. The cytosine was distinguished as CpG, CHG and CHH and the methylation levels were calculated separately.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph
 
Submission date Oct 19, 2020
Last update date Feb 04, 2021
Contact name Li Shen
E-mail(s) shenlab@zju.edu.cn
Phone 86-0571-88981751
Organization name Life Sciences Institute, Zhejiang University
Lab Shenlab
Street address 866 Yuhangtang Road
City Hangzhou
State/province Zhejiang Province
ZIP/Postal code 310058
Country China
 
Platform ID GPL17021
Series (1)
GSE159581 Role of CxxC-finger Protein 1 in the Establishment of Epigenetic Landscapes in Mouse Oocytes
Relations
BioSample SAMN16475156
SRA SRX9302847

Supplementary file Size Download File type/resource
GSM4832691_WGBS-GV-WT1.CG.bedGraph.gz 50.5 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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