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| Status |
Public on Aug 28, 2020 |
| Title |
Tri-4C: efficient and quantitative analysis of enhancer loops at hundred base pair resolution (Tri-4C) |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
Enhancer looping governs gene regulatory circuitry but is challenging to detect. Here we present Tri-4C, an ultrafine mapping method for distal chromatin contacts using triple restriction enzyme (RE) digestion. Tri-4C identifies enhancer loops that are undetectable by current single RE- based methods and reveals quantitative loop strengths in enhancer interaction networks underlying dynamic gene control. This multi-RE approach may be applied to general 3C-derived methods for accurate detection of enhancer loops.
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| Overall design |
Examination of long range chromatin interaction in IFNB1 locus in IMR90 cells.
Examination of long range chromatin interaction of ECAD9 in H7-derived vascular smooth muscle cells.
Examination of long range chromatin interaction of IMR90 using Tri-4C with alternative (CviAII) digestion.
The file "GSE119187_sample_viewpoints.xlsx" at the foot of this record includes the method (4C or Tri-4C) and the viewpoint sequence for each sample"
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| Contributor(s) |
Zhu Y, Suh Y |
| Citation missing |
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| Submission date |
Aug 29, 2018 |
| Last update date |
Aug 30, 2020 |
| Contact name |
Yizhou Zhu |
| E-mail(s) |
yizhou.zhu@phd.einstein.yu.edu
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| Organization name |
Albert Einstein College of Medicine
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| Department |
Genetics
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| Lab |
Yousin Suh
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| Street address |
Price469 1301 Morris Park Ave
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| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
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| Platforms (2) |
| GPL15520 |
Illumina MiSeq (Homo sapiens) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (38)
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| This SubSeries is part of SuperSeries: |
| GSE119189 |
Tri-4C: efficient and quantitative analysis of enhancer loops at hundred base pair resolution |
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| Relations |
| BioProject |
PRJNA488421 |
| SRA |
SRP159073 |
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