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| Status |
Public on May 11, 2018 |
| Title |
CTCF and Cohesin (Rad21) ChIP-seq in male mouse liver |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Sequencing files provided here include mouse liver ChIP-seq for CTCF and the cohesin subunit Rad21. These files are part of a larger study where we describe features of Topologically Associating Domains (TADs) and their impact on liver gene expression, then use these features to computationally predict subTAD structures not otherwise readily identifiable due to the low resolution of Hi-C. Our findings reveal that CTCF-based subTAD loops maintain key insulating properties of TADs, and support the proposal that subTADs are formed by the same loop extrusion mechanism and contribute to nuclear architecture as intra-TAD scaffolds that further constrain enhancer-promoter interactions. This allows high expression of super enhancer target genes and individual genes within inactive TADs, and may be a broadly conserved mechanism of genomic regulation.
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| Overall design |
CTCF and Cohesin (Rad21) ChIP-seq in mouse liver
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| |
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| Contributor(s) |
Matthews BJ, Shin A, Waxman DJ |
| Citation(s) |
29757144, 32680543 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 DK033765 |
Regulation of Sex Differences in Liver Metabolism |
BOSTON UNIVERSITY CHARLES RIVER CAMPUS |
DAVID J WAXMAN |
| R01 ES024421 |
Epigenetic Actions of Environmental Chemicals |
BOSTON UNIVERSITY CHARLES RIVER CAMPUS |
DAVID J WAXMAN |
|
| Submission date |
Aug 23, 2017 |
| Last update date |
Jul 27, 2020 |
| Contact name |
David J. Waxman |
| E-mail(s) |
djw@bu.edu
|
| Organization name |
Boston University
|
| Department |
Department of Biology and Bioinformatics Program
|
| Street address |
5 Cummington Mall
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
|
| Samples (7)
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| This SubSeries is part of SuperSeries: |
| GSE102999 |
Computational prediction of CTCF/cohesin-based intra-TAD (sbTAD) loops that insulate chromatin contacts and gene expression in mouse liver |
|
| Relations |
| BioProject |
PRJNA399718 |
| SRA |
SRP116021 |
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