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| Status |
Public on Mar 14, 2018 |
| Title |
The transcription start site and enhancer landscape of the descending colon in inflammatory bowel disease |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Inflammatory bowel disease (IBD) is a common and chronic gut disorder, with two subtypes: Crohn's disease (CD) and ulcerative colitis (UC), which are challenging to diagnose. The molecular pathology IBD is not well understood, and the underlying gene regulatory regions have not been comprehensively investigated. Relatedly, most IBD-associated SNPs are located in non-coding regions, and may effect gene regulation. Here, we profiled genome-wide promoter and enhancer activity in the descending colon of IBD patients. IBD-induced enhancer and promoters are highly enriched for IBD-associated SNPs, and can predict IBD diagnosis with an accuracy of 85% in an external cohort.
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| Overall design |
This experiment includes a total of 94 patients: 25 patients with active UC(UCa), 17 patients with UC in remission(UCi), 20 patients with active CD(CDa), 3 patients with CD in remission(CDi) and 29 healthy controls (Ctrl).
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| Contributor(s) |
Sandelin A |
| Citation(s) |
29695774 |
| |
| Submission date |
Feb 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Morana Vitezic |
| E-mail(s) |
mvitezic@gmail.com
|
| Organization name |
University of Copenhagen
|
| Department |
Department of Biology
|
| Lab |
Sandelin Lab
|
| Street address |
Ole Maaloes Vej 5
|
| City |
Copenhagen N |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (94)
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| Relations |
| BioProject |
PRJNA377127 |
| SRA |
SRP100787 |
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