Ranked GEO Datasets

Collections related to this search

Explore premium collections with reusable study, cohort and sample curation. The matching scope is stated for each collection. Organism, tissue, comparison and sample requirements still need review; collection availability does not affect dataset ranking.

IBD Colon Tissue Expression Collection

Disease scope matches your disease term.

Public colon tissue expression datasets for IBD, Crohn's disease, and ulcerative colitis.

Preview fixture · Version v0.1-preview

Study inventory: 3 datasets
Reported sample inventory: 522 samples
Updated: 2026-06-22
Disease: Inflammatory bowel disease
Organisms: Homo sapiens
Technologies: microarray, bulk RNA-seq
Tissues: colon biopsy, inflamed colon tissue, non-inflamed colon tissue
Comparisons: IBD vs non-IBD control, inflamed vs non-inflamed tissue, Crohn's disease vs ulcerative colitis

Query overlap with this collection version
Dimension	Your query	Collection scope	Comparison
Disease	Inflammatory bowel disease	Inflammatory bowel disease	MATCH Declared collection scope includes this requested dimension; question-specific sample eligibility still needs review.
Specimen		colon biopsy, inflamed colon tissue, non-inflamed colon tissue	NOT_REQUESTED No explicit query requirement was supplied for this dimension.
Organism		Homo sapiens	NOT_REQUESTED No explicit query requirement was supplied for this dimension.
Comparison		IBD vs non-IBD control, inflamed vs non-inflamed tissue, Crohn's disease vs ulcerative colitis	NOT_REQUESTED No explicit query requirement was supplied for this dimension.

Full access adds reusable curated cohort structure, sample decisions and provenance. Review the content status above before treating a release as professionally approved. Ordinary Search results remain available below.

Preview collection

Counts describe the collection inventory, not final eligible samples or independent subjects. Preview fixtures are illustrative; review-pending releases are not professionally approved.

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15 shown of 146 matching datasets Comparison Tumor vs normal Tissue/sample context Patient tissue Organism Any organism Assay Any assay Ranking defaults Modified 6 user changes 1 active filters Page 9 of 10 · showing 121-135

Disease/condition e.g. colorectal cancer Anatomical source Specimen material Cell population Comparison type (required) Organism Assay type Minimum samples Experimental model Exclude cell lines Require processed data GEO only recount3 available Expression Atlas available

Treatment requirements Optional See what each comparison arm must satisfy — Unrestricted

Comparison: Tumor vs normal

Case arm

Your requirement

Exposure state

Agent

Comparator

From comparison

Determined by comparison

For treatment vs control, use a named agent, an explicit collection window and an exposed or unexposed state. The comparator needs the opposite reported exposure state for the same agent, target and window.

Collection window Assertion target

Named agent if supplied; otherwise all interventions.

Scope & matching · additional options

Exposure scopeAutomatic: named agent if supplied; otherwise all interventions. Uncertain alternativesReview cases are not confirmed matches. Exact reported scope (when requested)

Missing metadata never proves no exposure.

Evidence and comparison rules

Exact results require an eligible sample subset and reported independent subjects in both arms.

“No exposure” applies only to the selected agent, target and time window. No exposure to a new agent before collection does not rule out earlier therapy.

A broader treatment history requires separate, explicit evidence and may be unavailable. All prior therapy requires a through-collection window.

Planned exposure does not establish that treatment occurred. Treatment vs control requires an exposed or unexposed state, a named agent and an explicit collection window.

Organism and specimen requirements apply to both arms. For treatment vs control, disease requirements also apply to both arms.

Genotype requirements Optional Define a requirement, then assign it to samples — Unrestricted

Genetic state Gene symbol

Apply requirement to

Specific protein variant · optional

Exact reported protein variant

Leave blank for a gene-level requirement. A variant restriction applies to every selected arm.

Genotype describes sampled material. Confirmed evidence must come from the same samples as your other requirements.

Use with human bulk RNA-seq or expression microarray.

Evidence and comparison rules

Select Homo sapiens and a supported assay in the search filters.

Missing genotype does not establish wild type. Both comparison arms still need eligible, independent samples.

A subject's carrier status does not establish the sampled tumor's genotype or disease.

Clear filters Ranking defaults Relax defaults

Showing one page of matching results. Use next/previous for browsing, or CSV/Markdown export for the full matching set.

Strict results

These datasets meet every active search criterion.

Bulk RNA-seq of whole biopsies and enteroids/colonoids from terminal ileum and rectum of inflammatory bowel disease patients or control subjects

Select

Organization: Children's hospital of Philadelphia

Case mixed disease cohort Control unclear

Unclear study design Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because study design or specimen source is unclear.
Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 37736163.

critical No clear control group was detected from normalized metadata. warning Multiple sample type labels or exclusion flags were detected. warning Organoid samples appear to be included. info Ambiguous sample metadata was detected in 1 sample(s): GSM7114773 matched "disease state: NA". Review these samples before inclusion or manual group assignment. warning Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Colonic mucosal gene expression profile associated with neoplastic progression in longstanding ulcerative colitis

Select

Organization: University of Oslo

Case inflamed tissue Control unclear

Unclear study design Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because study design or specimen source is unclear.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Colorectal cancer, Inflammatory bowel disease, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 40989939.

critical No clear control group was detected from normalized metadata. info Microarray expression context was detected; compare separately from RNA-seq cohorts. warning Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Blood gene expression biomarkers of response to anti-TNF drugs in pediatric patients before initiation of treatment

Select

Organization: Hospital General Universitario Gregorio Marañón

Case inflammatory bowel disease Control unclear

Unclear study design Biofluid

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because it is a biofluid cohort.
Downgraded for tissue search because study design or specimen source is unclear.
Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Inflammatory bowel disease.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 38401525.

critical No clear control group was detected from normalized metadata. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Transcription levels in human colon biopsies in IBS and IBD patients before and after participating in a high red-meat dietary intervention

Select

Organization: Maastricht University

Case mixed disease cohort Control unclear

Unclear study design Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because study design or specimen source is unclear.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Colorectal cancer, Inflammatory bowel disease.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 21669488.

critical No clear control group was detected from normalized metadata. info Microarray expression context was detected; compare separately from RNA-seq cohorts. warning Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. warning Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Gene expression patterns of biopsies from a colonoscopy taken in 2007 of an ulcerative colitis patient infected with Trichuris trichiura

Select

Organization: UCSF

Case ulcerative colitis Control unclear

Unclear study design Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because study design or specimen source is unclear.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Infectious disease or host response, Inflammatory bowel disease, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 21123809.

critical No clear control group was detected from normalized metadata. info Microarray expression context was detected; compare separately from RNA-seq cohorts. warning Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Gene expression patterns of biopsies from a colonoscopy taken in 2008 of an ulcerative colitis patient infected with Trichuris trichiura

Select

Organization: UCSF

Case ulcerative colitis Control unclear

Unclear study design Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because study design or specimen source is unclear.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Infectious disease or host response, Inflammatory bowel disease, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 21123809.

critical No clear control group was detected from normalized metadata. info Microarray expression context was detected; compare separately from RNA-seq cohorts. warning Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Gene expression patterns of biopsies from a colonoscopy taken in 2009 of an ulcerative colitis patient infected with Trichuris trichiura

Select

Organization: UCSF

Case ulcerative colitis Control unclear

Unclear study design Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because study design or specimen source is unclear.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Infectious disease or host response, Inflammatory bowel disease, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 21123809.

critical No clear control group was detected from normalized metadata. info Microarray expression context was detected; compare separately from RNA-seq cohorts. warning Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Clinical and molecular characterization of steatotic liver disease in the setting of immune-mediated inflammatory diseases

Select

Organization: Instituto de Investigación Marqués de Valdecilla

Case mixed disease cohort Control unclear

Unclear study design Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because study design or specimen source is unclear.
Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Fibrosis, Inflammatory bowel disease, Liver fibrosis, Metabolic disease, Steatohepatitis (NASH/MASH), Steatotic liver disease (NAFLD/MASLD), Type 2 diabetes.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 39411649.

critical No clear control group was detected from normalized metadata. warning Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Gene expression dysregulation in whole blood of patients with C. difficile infection

Select

Organization: University of Liverpool

Case mixed disease cohort Control unclear

Unclear study design Biofluid

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because it is a biofluid cohort.
Downgraded for tissue search because study design or specimen source is unclear.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Infectious disease or host response, Inflammatory bowel disease.
Processed data is available for downstream review.
External evidence: PubMed links 2 publications; 2 DOIs available: PMID 39684365, PMID 39894009.

critical No clear control group was detected from normalized metadata. info Microarray expression context was detected; compare separately from RNA-seq cohorts. warning Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. warning Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

eQTL in diseased colon tissue identifies novel target genes associated with IBD

Select

Organization: University of North Carolina at Chapel Hill

Case inflammatory bowel disease Control unclear

Unclear study design Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because study design or specimen source is unclear.
Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Inflammatory bowel disease.
Processed data is available for downstream review.
External evidence: PubMed links 2 publications; 2 DOIs available: PMID 39464142, PMID 41688467.

critical No clear control group was detected from normalized metadata. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Reference-guided genome assembly of long non-coding RNA transcripts reveals target genes associated with Crohn’s disease

Select

Organization: University of North Carolina at Chapel Hill

Case mixed disease cohort Control non-inflamed tissue

Unclear study design Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because study design or specimen source is unclear.
Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 42185506.

warning Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. warning Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Comparison of intestinal surface CD3- refractory celiac disease type II (RCDII) cell lines with intestinal surface CD3+ cell lines of non-RCDII patients

Select

Organization: LUMC

Case Crohn's disease Control unclear

Unclear study design Cell line

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because it is a model-system experiment.
Downgraded for tissue search because study design or specimen source is unclear.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Crohn's disease.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 22760007.

critical No clear control group was detected from normalized metadata. warning Multiple sample type labels or exclusion flags were detected. warning Cell line samples appear to be included. info Microarray expression context was detected; compare separately from RNA-seq cohorts. warning Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Distinct, non-overlapping gene panels of peripheral blood gene expression predict response to infliximab therapy in rheumatoid arthritis and Crohn's disease

Select

Organization: University of Debrecen

Case mixed disease cohort Control unclear

Unclear study design Biofluid

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because it is a biofluid cohort.
Downgraded for tissue search because study design or specimen source is unclear.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Crohn's disease, Rheumatoid arthritis.
Processed data is available for downstream review.
External evidence: PubMed links 2 publications; 2 DOIs available: PMID 23809696, PMID 32104045.

critical No clear control group was detected from normalized metadata. info Microarray expression context was detected; compare separately from RNA-seq cohorts. warning Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. warning Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Gene expression analysis of omental and mesenteric adipose tissue in Crohn's disease and ulcerative colitis

Select

Organization: istituto auxologico italiano

Case mixed disease cohort Control unclear

Unclear study design Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because study design or specimen source is unclear.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 24205244.

critical No clear control group was detected from normalized metadata. info Microarray expression context was detected; compare separately from RNA-seq cohorts. warning Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. warning Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Gene expression of human small intestine generated by biopsy specimens

Select

Organization: Tokyo Medical and Dental University

Case mixed disease cohort Control unclear

Unclear study design Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because study design or specimen source is unclear.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease.
Processed data is available for downstream review.
External evidence: Expression Atlas curated experiment link is available.
External evidence: PubMed links 2 publications; 2 DOIs available: PMID 26891258, PMID 39159791.

critical No clear control group was detected from normalized metadata. info Microarray expression context was detected; compare separately from RNA-seq cohorts. warning Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. warning Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.