GEO DataSets

Analysis of colonoscopic biopsies from patients with Crohn’s disease (CD) or ulcerative colitis (UC). CD and UC are inflammatory bowel diseases with variable, overlapping clinical features and complex pathophysiologies. Results provide insight into the pathogenesis of CD and UC.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 5 disease state, 3 specimen sets

Platform:

GPL8300

Series:

GSE6731

36 Samples

Download data: CEL, EXP

(Submitter supplied) Ulcerative colitis (UC) and Crohn’s disease (CD) are inflammatory bowel diseases (IBD) with variable, overlapping clinical features and complex pathophysiologies. To identify pathogenic processes underlying these disease subtypes, using single endoscopic pinch biopsies to estabolish 36 expression profiles, we elucidated gene expression patterns of active and inactive areas of UC and CD, and compared these to infectious colitis and healthy controls. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS2642

Platform:

GPL8300

36 Samples

Download data: CEL, EXP

(Submitter supplied) The aim of this study is to identify early pathogenic changes in ileal gene expression that precede the development of macroscopic disease in inflammatory bowel diseases (IBDs). We focused on two IBD phenotypes that were unlikely to overlap: 1) ileal Crohn’s disease (CD) patients undergoing initial ileocolic resection of diseased ileum; and 2) ulcerative colitis (UC) patients undergoing total colectomy. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

99 Samples

Download data: GPR

(Submitter supplied) Ulcerative colitis (UC) is a chronic inflammatory disease of the colon with preiods of active disease followed by remission. We performed a whole-genome transcriptional analysis of colonic biopsies from patients with histologically active and inactive UC, as well as non-inflammatory controls.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4365

Platform:

GPL570

43 Samples

Download data: CEL

Analysis of colonic biopsies from patients with histologically active or inactive UC and from healthy, non-inflammatory controls. UC is a chronic inflammatory disease with periods of active disease followed by remission. Results provide insight into molecular events associated with UC remission.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 5 agent, 4 disease state sets

Platform:

GPL570

Series:

GSE38713

43 Samples

Download data: CEL

(Submitter supplied) Background and aims: Mucosal abnormalities are potentially important in the primary pathogenesis of ulcerative colitis (UC). We investigated the mucosal transcriptomic expression profiles of biopsies from patients with UC and healthy controls (HC), taken from macroscopically non-inflamed tissue from the terminal ileum and three colonic locations with the objective of identifying abnormal molecules that might be involved in disease development. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

171 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling of Crohn's disease, ulcerative colitis, and normal colon mucosa samples. The Illumina Infinium HumanMethylation450 BeadChip v1.1 was used to obtain DNA methylation profiles across 482,421 CpGs in colon mucosa samples. Samples came from 5 Crohn's disease affected, 5 ulcerative colitis affected, and 12 normal individuals. One ulcerative colitis sample was assayed before and after treatment with infliximab and mesalamine.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

23 Samples

Download data: TXT

(Submitter supplied) Genome wide expression profiling of ulcerative colitis, and normal colon mucosa samples. The GeneChip PrimeView Human Gene Expression Array was used to obtain expresion profiles across colon mucosa samples. Samples came from 5 ulcerative colitis affected, and 5 normal individuals.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

10 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

73 Samples

Download data

(Submitter supplied) Genome wide DNA methylation profiling of Crohn's disease, ulcerative colitis, and normal colon mucosa samples. The Illumina Infinium HumanMethylation450 BeadChip v1.1 was used to obtain DNA methylation profiles across 482,421 CpGs in colon mucosa samples. Samples came from 10 Crohn's disease affected, 4 ulcerative colitis affected, and 10 normal individuals. One ulcerative colitis sample was assayed before and after treatment with 6-mercaptopurine and mesalamine.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

25 Samples

Download data: TXT

(Submitter supplied) The series was designed to identify new genes involved in the pathophysiology of inflammatory bowel disease (Crohn's disease and ulcerative colitis). This series represents a group of 31 samples, subdivided into 3 groups: 1) Normal controls: 11 samples; 2) patients with Crohn's diseases: 10 samples; 3) patients with ulcerative colitis: 10 samples. Each sample originated from a different patient or normal control, in total n=31 individuals were examined. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS1330

Platform:

GPL284

31 Samples

Download data

Expression profiling of mucosal biopsy samples from sigmoid colons of 10 patients with Crohn disease (CD) and 10 patients with ulcerative colitis (UC). CD and UC are two forms of inflammatory bowel disease. Results provide insight into the pathogenesis of CD and UC.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 3 disease state sets

Platform:

GPL284

Series:

GSE1710

31 Samples

Download data

(Submitter supplied) Background and Aims: Crohn’s disease [CD] and ulcerative colitis [UC] are distinct forms of inflammatory bowel disease. Heterogeneity of HLA-DR+SIRPα + mononuclear phagocytes [MNPs], including macrophages [MΦ], monocyte-derived [Mono] cells, and dendritic cells [DCs], was reported in gut tissue but not yet investigated in mesenteric lymph nodes [MLNs] of IBD patients. We here compared the phenotype, function, and molecular profile of HLA-DR+SIRPα+ MNPs in CD and UC MLNs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

22 Samples

Download data: TXT

(Submitter supplied) The drug targets IL23 and IL12 regulate pathogenicity and plasticity of intestinal Th17 cells in Crohn’s disease (CD) and ulcerative colitis (UC), the two most common inflammatory bowel diseases (IBD). However, studies examining Th17 dysregulation in mesenteric lymph nodes (mLNs) of these patients are rare. We showed that in mLNs, CD could be distinguished from UC by increased frequencies of CCR6+CXCR3-RORg+Tbet-CD4+ (Th17) memory T cells enriched in CD62Llow effector memory T cells (TEM), and their differentially expressed molecular profile. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL21847

12 Samples

Download data: RCC

(Submitter supplied) These samples were all taken from patients who underwent investigations including colonoscopy but where all tests were normal and the diagnosis of irritable bowel syndrome was reached. These observations have been used as references in studies of colonic gene expression in inflammatory bowel diseases

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

17 Samples

Download data: CEL

(Submitter supplied) The samples are a part of a study aiming at diagnosing ulcerative colitis from genome-wide gene expression analysis of the colonic mucosa. Colonic mucosal samples were collected as endoscopic pinch biopsies from ulcerative colitis patients and from control subjects. Samples with and without macroscopic signs of inflammation were collected from the patients. Keywords: Disease state analysis

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3119

Platform:

GPL570

26 Samples

Download data: CEL

Analysis of colonic mucosa samples with or without signs of inflammation from patients with ulcerative colitis (UC), a type of inflammatory bowel disease (IBD). Results provide insight into the molecular mechanisms contributing to the development of inflammation in UC.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 disease state, 2 specimen sets

Platform:

GPL570

Series:

GSE9452

26 Samples

Download data: CEL

(Submitter supplied) USeq software package identified 44 microRNAs with altered expression (fold change ≥2 and false discovery rate ≤0.10) compared to controls. Among them, a panel of 11 microRNAs was aberrantly expressed between UC and CD. qRT-PCR validation assays performed on frozen tissue from additional samples of UC (n=20) and CD (n=10) confirmed specific differential expression of miR-147b, miR-194-2, miR-383, miR-615 and miR-1826 (P<0.05). more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

37 Samples

Download data: XLS

(Submitter supplied) To find predictive biomarkers for the development from inflammatory bowel disease unclassified (IBDU) to Crohn's disease(CD) or ulcerative colitis (UC), we performed short non-coding RNA profiling on IBDU patient samples at the time of diagnostic endoscopy.

Organism:

Homo sapiens; synthetic construct

Type:

Non-coding RNA profiling by array

Platform:

GPL19117

43 Samples

Download data

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

94 Samples

Download data: BED