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| Status |
Public on Dec 01, 2020 |
| Title |
Genome-wide chromatin interactions identify characteristic promoter-distal loops |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
We developed a novel computational model, HiSIF (Hi-C Significant Interacting Fragments), which uses a Poisson Mixture Model (PMM) with a power-law decay background. We compared its performance to some existing programs with publicly available Hi-C data, and then applied it to in situ Hi-C data in breast cancer sensitive and resistant cells.
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| Overall design |
In this study, we tested the model in our newly generated Hi-C data in three ERĪ± positive breast cancer cell lines, MCF7, tamoxifen-resistant MCF7 (MCF7-TamR) (MCF7 and MCF7-TamR data have been deposited in GEO under accession number GSE108787), T47D and tamoxifen-resistant T47D (T47D-TamR), ZR75-1 and tamoxifen-resistant ZR75-1 (ZR75-1-TamR).
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| Contributor(s) |
Zhou Y, Jin V |
| Citation(s) |
32956836 |
| Submission date |
Mar 21, 2019 |
| Last update date |
Dec 01, 2020 |
| Contact name |
Yufan Zhou |
| Organization name |
UT health Science Center at San Antonio
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| Street address |
7703 Floyd Curl Dr
|
| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
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| Platforms (1) |
| GPL21290 |
Illumina HiSeq 3000 (Homo sapiens) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA528483 |
| SRA |
SRP189090 |
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