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| Status |
Public on Feb 04, 2021 |
| Title |
WGBS-GV-WT3 |
| Sample type |
SRA |
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| Source name |
WT mouse GV oocytes
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| Organism |
Mus musculus |
| Characteristics |
stain: C57BL/6
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| Treatment protocol |
4 week mouse treated by PMSG 44 h
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| Growth protocol |
in vivo
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| 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 |
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| 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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| Submission date |
Oct 19, 2020 |
| Last update date |
Feb 04, 2021 |
| Contact name |
Li Shen |
| E-mail(s) |
shenlab@zju.edu.cn
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| Phone |
86-0571-88981751
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| Organization name |
Life Sciences Institute, Zhejiang University
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| Lab |
Shenlab
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| Street address |
866 Yuhangtang Road
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| City |
Hangzhou |
| State/province |
Zhejiang Province |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE159581 |
Role of CxxC-finger Protein 1 in the Establishment of Epigenetic Landscapes in Mouse Oocytes |
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| Relations |
| BioSample |
SAMN16474405 |
| SRA |
SRX9302849 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4832693_WGBS-GV-WT3.CG.bedGraph.gz |
51.4 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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