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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 26, 2021 |
| Title |
A compendium map of Cis-Regulatory Elements in the Pig Genome and epigenetic comparison with the human Genome |
| Organism |
Sus scrofa |
| Experiment type |
Other
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Although major advances in genomics have initiated an exciting new era of research, the lack of information about cis-regulatory elements has limited the genetic improvement or manipulation of pig as meat source and biomedical model. Here, we systematically characterize the cis-regulatory elements and their functions in the pig genome in 12 diverse tissues from 4 pig breeds through RNA-Seq, ATAC-Seq, and ChIP-Seq analyses. In total, we generated 199 datasets and identified more than 220,000 pig cis-regulatory elements. We find that cis-regulatory elements are more conserved between humans and pigs than that between humans and mice. To further explore the three dimension structure of pig genome, we performed high-throughput chromosome conformation capture (Hi-C) experiment. The rearrangements of TADs between pig and human have apparently contributed to the evolution of head and face phenotypes. Beyond generating a major new benchmark resource for pig epigenetics research, our study provides basic epigenetic comparative data for using pig as a model for human biomedical research.
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| Overall design |
High-throughput sequencing (RNA-seq, ChIP-Seq, ATAC-seq, and Hi-C)of diverse tissues from four pig breeds.
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| Contributor(s) |
Zhao Y, Hou Y, Xu Y, Zhao S |
| Citation(s) |
33850120, 35681201 |
| BioProject |
PRJNA597497 |
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| Submission date |
Jan 08, 2020 |
| Last update date |
Jun 24, 2022 |
| Contact name |
Shuhong Zhao |
| E-mail(s) |
shzhao@mail.hzau.edu.cn
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| Organization name |
Huazhong Agricultural University
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| Street address |
No.1,Shizishan Street, Hongshan District
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| City |
Wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
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| Platforms (1) |
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| Samples (200)
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| Relations |
| SRA |
SRP238708 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE143288_RAW.tar |
100.3 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH, BIGWIG, NARROWPEAK) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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