|
| Status |
Public on May 01, 2019 |
| Title |
MethylC_FGO_Dnmt3l_KO_5mC_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
oocyte
|
| Organism |
Mus musculus |
| Characteristics |
tissue: oocyte
developmental stage: FGO
genotype: Dnmt3l_KO
|
| Treatment protocol |
8-week-old females were intraperitoneally injected with PMSG and hCG. Oocytes and embryos were harvested in M2 medium at following time point after hCG: MII oocytes, 13h; Zygotes 30 h; late-two cell embryos, 47 h; blastocyts 98h, Germinal vesicle stage
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The DNA extraction follows STEM-seq protocol
The STEM-seq libraries were generated following the protocol as described previously(Zhang et al., 2018).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
processed data file:
FGO_Dnmt3l_KO_5mC.bed.gz
|
| Data processing |
STEM-seq datasets were trimmed adaptors by Trim galore and then aligned to the mm9 reference genome though BSSeeker2 with the parameters: --bt2-p 8 --XS 0.2,3 --a CCCCCC --m 4. Multiple mapped and duplicated reads were also removed.
Genome_build: mm9
Supplementary_files_format_and_content: For STEM-seq, the bedgraph files contains the average DNA methylation level of 2kb bin.
|
| |
|
| Submission date |
Apr 06, 2018 |
| Last update date |
May 01, 2019 |
| Contact name |
Wei Xie |
| E-mail(s) |
xiewei121@tsinghua.edu.cn
|
| Organization name |
Tsinghua University
|
| Department |
School of Life Science
|
| Street address |
Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE112833 |
SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development [Bisulfite-seq] |
| GSE112835 |
SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development |
|
| Relations |
| BioSample |
SAMN08887586 |
| SRA |
SRX3899476 |
