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| Status |
Public on Apr 13, 2018 |
| Title |
E75Exe_WGBS |
| Sample type |
SRA |
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| Source name |
mouse embryo
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| Organism |
Mus musculus |
| Characteristics |
tissue: 7.5 day embyo extraembryonic ectoderm
strain: C57BL/6 x DB/2
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| 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
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
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| 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.
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| Submission date |
Apr 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Shaorong Gao |
| Organization name |
Tongji University
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| Department |
School of life science and technology
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| Lab |
Gaolab
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| Street address |
1239 Siping Road, Yangpu District
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
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| 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] |
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| Relations |
| BioSample |
SAMN06829146 |
| SRA |
SRX2763347 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2588719_E75Exe.bsmap.CpG.txt.gz |
160.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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