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Series GSE95437 Query DataSets for GSE95437
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
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.
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).
Contributor(s) Sandelin A
Citation(s) 29695774
Submission date Feb 27, 2017
Last update date May 15, 2019
Contact name Morana Vitezic
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
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (94)
GSM2511540 CD_a102
GSM2511541 CD_a103
GSM2511542 CD_a107
BioProject PRJNA377127
SRA SRP100787

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE95437_RAW.tar 1.4 Gb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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