Ranked GEO Datasets

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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.

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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 2 of 10 · showing 16-30

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.

A systems biology approach identifies ANP32E and other biomarkers of glucocorticoid refractoriness in ulcerative colitis [miRNA-Seq]

Select

Organization: CIC bioGUNE

Case ulcerative colitis Control healthy control

Disease/model vs control Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 30329026.

warning Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. 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.

Inflammatory bowel disease

Select

Organization: Institute of Human Genetics

Case Crohn's disease Control control

Disease/model vs control Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis.
Processed data availability is missing or unclear.
External evidence: PubMed links 2 publications; 2 DOIs available: PMID 17058067, PMID 17461471.

warning Processed count data was not found in the dataset index. 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.

Common functional alterations identified in blood transcriptome of autoimmune cholestatic liver and inflammatory bowel diseases

Select

Organization: Uniwersytet Warszawski

Case mixed disease cohort Control control

Disease/model vs control 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 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 13 publications; 13 DOIs available: PMID 31076612, PMID 34545326, PMID 35741659, PMID 37784152, PMID 37844121.

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.

Concordance between gene expression in peripheral whole blood and colonic tissue in children with inflammatory bowel disease.

Select

Organization: Boston Children's Hospital

Case Crohn's disease Control control

Disease/model vs control Mixed specimen/source

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because specimen/source classes are mixed.
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 12 publications; 11 DOIs available: PMID 31618209, PMID 33585004, PMID 34592880, PMID 34786719, PMID 36792688.

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 tissue or biopsy source clarity.

Transcriptional signatures that define Ulcerative Colitis in remission

Select

Organization: Universiry of Tromso

Case mixed disease cohort Control healthy control

Disease/model vs control Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 3 publications; 3 DOIs available: PMID 32322884, PMID 37199828, PMID 38514698.

warning Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.

Differential pathogenic Th17 profile in mesenteric lymph nodes of Crohn's disease and ulcerative colitis patients

Select

Organization: CRCHUM

Case mixed disease cohort Control control

Disease/model vs control Unclear specimen/source

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 31191543.

Expression Profiles of Circular RNAs in colon biopsies from Crohn’s Disease Patients by Microarray Analysis

Select

Organization: Jinling Hospital, Nanjing University School of Medicine

Case ulcerative colitis Control healthy control

Disease/model vs control Unclear specimen/source

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, Ulcerative colitis.
Processed data is available for downstream review.

Gene expression data from a cohort of Chilean Ulcerative Colitis human intestinal samples

Select

Organization: NIEHS

Case inflamed tissue Control non-inflamed tissue

Disease/model vs control Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Inflammatory bowel disease, Ulcerative colitis.
Processed data is available for downstream review.

Ulcerative colitis gene expressions file

Select

Organization: The Third Affiliated Hospital of Sun Yat-Sen University

Case ulcerative colitis Control healthy control

Disease/model vs control Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 4 publications; 3 DOIs available: PMID 32015337, PMID 34925026, PMID 36631011, PMID 39993549.

Human macrophage responses to viral-like particles from non-IBD or IBD colonic resections

Select

Organization: Massachusetts General Hospital

Case mixed disease cohort Control mixed controls

Disease/model vs control Unclear specimen/source

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 35394816.

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 tissue or biopsy source clarity.

Ileum Transcriptomic Profiling in Inflammatory Bowel Disease

Select

Organization: Georgia Institute of Technology

Case mixed disease cohort Control control

Disease/model vs control Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

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 2 publications; 2 DOIs available: PMID 32058087, PMID 40808866.

warning Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.

RNA profiles in serum and urine extracellular vesicles of patients with cholangiocarcinoma mimicking tumor expression: novel liquid biopsy approach

Select

Organization: CIC bioGUNE

Case mixed disease cohort Control healthy control

Patient biofluid vs healthy control 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 assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Other non-gastrointestinal cancer, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 32183400.

warning Multiple sample type labels or exclusion flags were detected. warning Cell line samples appear to be included. warning Extracellular vesicle or exosome context was detected and may not represent ordinary tissue bulk RNA-seq. 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.

Mucosal gene signatures to predict response to infliximab in patients with ulcerative colitis

Select

Organization: KULeuven

Case ulcerative colitis Control control

Disease/model vs control Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Ulcerative colitis.
Processed data is available for downstream review.
External evidence: Expression Atlas curated experiment link is available.
External evidence: PubMed links 7 publications; 7 DOIs available: PMID 19700435, PMID 31886172, PMID 35102110, PMID 35876170, PMID 36983834.

Comprehensive transcriptome profiling of ulcerative colitis mouse model suggests biomarkers and therapeutic targets for human colitis [RNA-Seq]

Select

Organization: Steno Diabetes Center Copenhagen

Case ulcerative colitis Control control

Disease/model vs control Biofluid

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because it is a biofluid cohort.
Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Inflammatory bowel disease, Ulcerative colitis.
Processed data is available for downstream review.

warning Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. critical Dataset organism does not match the human patient-tissue tumor-normal intent.

Analysis of Gene Expression changes in human intestinal endothelial-to-mesenchymal transition - TRANSFORMED GROUP

Select

Organization: Cleveland Clinic

Case mixed disease cohort Control healthy control

Disease/model vs control Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Crohn's disease, Fibrosis, Inflammatory bowel disease, Ulcerative colitis.
Processed data is available for downstream review.

warning Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review. 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.