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| Status |
Public on Jul 02, 2020 |
| Title |
The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos [ChIP-seq] |
| Organism |
Sus scrofa |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Pigs are important animals for agricultural and biomedical research, and its assisted reproductive technologies are urgently needed to be improved. Determining the underlying mechanism of epigenetic reprogramming in the early stage of preimplantation embryos derived from in vitro fertilization (IVF), parthenogenesis (PA) and androgenesis (AG), will not only contribute to assisted reproduction technologies of pigs but also will shed light into early human development. We generated 3D chromatin profiles for pig somatic cells, IVF, PA and AG preimplantation embryos. We found that the chromosomes in the pig preimplantation embryos are enriched for superdomains, i.e., the larger than 10M compartment domains, which are much rarer in mice. Wheras, p(s) curves, compartments and TADs, are largely conserved in somatic cells, and are gradually establishing during preimplantation embryogenesis. In the uniparental pig embryos, the establishment of chromatin architecture was highly asynchronized at all levels from IVF embryos, and a remarkably strong decompartmentalization was observed during zygotic genome activation (ZGA). Finally, chromosomes originating from oocytes always establish TADs faster than chromosomes originating from sperm, both before and during ZGA.
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| Overall design |
We generated two histone modifications and CTCF binding profiles for pig embryonic fibroblasts (PEFs).
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| Contributor(s) |
Li F, Wang D, Song R, Cao C, Zhang Z, Wang Y, Li X, Huang J, Liu Q, Hou N, Xu B, Li X, Gao X, Jia Y, Zhao J, Wang Y |
| Citation(s) |
32778155 |
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| Submission date |
Jun 29, 2020 |
| Last update date |
Aug 24, 2020 |
| Contact name |
Feifei Li |
| E-mail(s) |
liff@big.ac.cn
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| Phone |
15101052702
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| Organization name |
Beijing Institute of Genomics
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| Street address |
Chaoyang West Road, No.1
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| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platforms (1) |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE153452 |
The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos |
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| Relations |
| BioProject |
PRJNA642744 |
| SRA |
SRP269170 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE153451_RAW.tar |
8.4 Mb |
(http)(custom) |
TAR (of NARROWPEAK) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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