|
Status |
Public on Feb 04, 2021 |
Title |
WGBS-GV-CZ1 |
Sample type |
SRA |
|
|
Source name |
Cxxc1fl/fl;Gdf9-Cre 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.
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|
|
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
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|
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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 |
SAMN16474404 |
SRA |
SRX9302850 |