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Sample GSM3084614 Query DataSets for GSM3084614
Status Public on May 01, 2019
Title MethylC_FGO_Setd2_KO_5mC_rep1
Sample type SRA
Source name oocyte
Organism Mus musculus
Characteristics tissue: oocyte
developmental stage: FGO
genotype: Setd2_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:
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
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
BioSample SAMN08887582
SRA SRX3899480

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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