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Sample GSM2588718 Query DataSets for GSM2588718
Status Public on Apr 13, 2018
Title E75Epi_WGBS
Sample type SRA
 
Source name mouse embryo
Organism Mus musculus
Characteristics tissue: 7.5 day embyo epiblast
strain: C57BL/6 x DB/2
Extracted molecule genomic DNA
Extraction protocol For MII oocyte and cleavage-stage embryos, the zona pellucida of embryos was removed by 0.5% pronase E (Sigma). Then the embryo was incubated in Ca2+ free CZB for 5 min. Polar bodies were removed by gentle pipetting using an inner diameter of 120 μm fire polished glass needle. For ICM and TE isolation, the zona pellucida of blastocysts was removed by 0.5% pronase E (Sigma). They were then incubated for 20 min in Ca2+ free CZB,the tight junctions TE cells and ICM cells were separated by gently pipetting in a pipette with a diameter of 40-60 μm.For epiblast (Epi) and extraembryonic ectoderm (Exe) isolation, embryos were cuttted at the embryonic/extraembryonic boundary using properly sharpened forceps. A fire-polished glass needle whose inner diameter is silghtly smaller than the width of the embryonic/extraembryonic fragment was used for separating epiblast or extraembryonic ectoderm from the visceral endoderm, and the epiblast or extraembryonic ectoderm were then incubated in Ca2+-free CZB for 10 min. Single cells were separated by gentle pipetting using a fire-polished glass needle with an inner diameter of 15-20 μm.100-200 cells were washed three times in 0.5% BSA-PBS solution for one reaction。
Libraries were prepared according to Pico Methyl-Seq™ Library Prep Kit (Zymo Research, D5456) following the manufacturer’s instructions
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model HiSeq X Ten
 
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using using bsmap(v 2.89) with parameter “--s 16 -v 0.1 -n 1 -R".
Methylation level of each CpG site was estimated using mcall(v 1.3.0) with default parameters, and output bed format files are transformed to tab-delimited text files using custom python scripts.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include methylation level and coverage for each CpG site.
 
Submission date Apr 25, 2017
Last update date May 15, 2019
Contact name Shaorong Gao
Organization name Tongji University
Department School of life science and technology
Lab Gaolab
Street address 1239 Siping Road, Yangpu District
City Shanghai
State/province Shanghai
ZIP/Postal code 200092
Country China
 
Platform ID GPL21273
Series (2)
GSE97778 Reprogramming of H3K9me3-dependent heterochromatin during mammalian early embryo development
GSE98151 Reprogramming of H3K9me3-dependent heterochromatin during mammalian early embryo development [WGBS]
Relations
BioSample SAMN06829147
SRA SRX2763346

Supplementary file Size Download File type/resource
GSM2588718_E75Epi.bsmap.CpG.txt.gz 156.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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