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Series GSE179285 Query DataSets for GSE179285
Status Public on Jul 26, 2021
Title Embark cross-sectional study of inactive and active lesions from the ileum and colon of inflammatory bowel disease patients
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Hypothesis: Gene expression differences in biopsies from patients with inflammatory bowel disease can be used to identify molecular heterogeneity within patients with active disease.
Methods: Patients with a diagnosis of Crohn's disease, ulcerative colitis or normal healthy controls (with or without infectious colitis) underwent ileocolonoscopy. In healthy controls, biopsies were taken in the sigmoid colon (n=21), ascending/descending colon (n=25) and the terminal ileum (n=12). In patients with Crohn's disease, biopsies were taken in the ascending/descending colon (n=107) and terminal ileum (n=70) in uninflamed areas in all patients; in patients with mucosal lesions, additional biopsies were taken in inflamed regions of the ascending/descending colon (n=35) and terminal ileum (n=55). In ulcerative colitis patients, paired uninflamed sigmoid (n=48) and inflamed sigmoid biopsies (n=46) were taken. Biopsies were placed in RNAlater at the clinical site, frozen and shipped to Genentech, where they were disrupted using TissueLyzer beads, then RNA was isolated using RNeasy columns. RNA was hybridized to Agilent human 4x44kv1 arrays, dual channel, using universal reference.
 
Overall design Intestinal biopsies were collected from active lesions and inactive adjacent regions in patients with either Crohn's disease or ulcerative colitis. Matched non-IBD controls with no obvious intestinal disease are included for comparison.
 
Contributor(s) Hackney JA, Keir ME
Citation(s) 34561227
Submission date Jul 01, 2021
Last update date Oct 25, 2021
Contact name Jason A Hackney
E-mail(s) hackney.jason@gene.com
Organization name Genentech, Inc.
Department Department of Bioinformatics and Computational Biology
Street address 1 DNA Way
City South San Francisco
State/province CA
ZIP/Postal code 94080
Country USA
 
Platforms (1)
GPL6480 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version)
Samples (254)
GSM5413223 1416_UC uninflamed sigmoid colon
GSM5413224 2204_UC uninflamed sigmoid colon
GSM5413225 1506_UC inflamed sigmoid colon
Relations
BioProject PRJNA743064

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
GSE179285_RAW.tar 3.5 Gb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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