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 5 of 10 · showing 61-75

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.

Contribution of Stroma to Inflammatory Bowel Disease Progression Revealed in Patient-Derived Human Colon Chips

Select

Organization: Harvard 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.

Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Crohn's disease, Fibrosis, Inflammatory bowel disease, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 2 publications; 2 DOIs available: PMID 39677416, PMID 39975910.

No warnings

Licochalcone B alleviates Crohn’s Disease injury by targeting FTO

Select

Organization: Anhui Medical University

Case inflammatory bowel disease Control healthy 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.
Processed data is available for downstream review.

critical Dataset organism does not match the human patient-tissue tumor-normal intent.

Licochalcone B alleviates Crohn’s Disease injury by targeting FTO [meRIP-seq]

Select

Organization: Anhui Medical University

Case inflammatory bowel disease Control healthy 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.
Processed data is available for downstream review.

critical Dataset organism does not match the human patient-tissue tumor-normal intent.

The RNA-seq of Ulcerative colitis patients and health

Select

Organization: West China Hospital of Sichuan University

Case ulcerative colitis 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.

No warnings

RNAseq of colonic epithelial and lamina propria-derived Tregs

Select

Organization: Amsterdam University Medical Center

Case Crohn's disease Control healthy 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: Colorectal cancer, Crohn's disease, Inflammatory bowel disease.
Processed data is available for downstream review.

No warnings

Comparison of PBMCs in Inflammatory Bowel Disease

Select

Organization: Wyeth

Case ulcerative colitis Control normal tissue

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 11 publications; 11 DOIs available: PMID 16436634, PMID 31618209, PMID 37291580, PMID 39006497, PMID 39712025.

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.

Gene expression profiles of pediatric IBD remission patients

Select

Organization: UMC Utrecht

Case inflammatory bowel disease 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: Inflammatory bowel disease.
Processed data is available for downstream review.
External evidence: PubMed links 3 publications; 3 DOIs available: PMID 24260248, PMID 29381010, PMID 39894009.

Genome-wide analysis of Crohn's disease and ulcerative colitis biopsy samples.

Select

Organization: Whilliam Harvey Research Institute, Bart's and The London School of Medicine; Queen Mary University of London

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.

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 21 publications; 21 DOIs available: PMID 24155895, PMID 30015893, PMID 32489050, PMID 34717557, PMID 35497913.

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.

Gene Expression Changes in Non-Dysplastic Mucosa from Patients with Ulcerative Colitis Harboring Remote Neoplastic Lesions

Select

Organization: University of Chicago

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: Colorectal cancer, Inflammatory bowel disease, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 4 publications; 4 DOIs available: PMID 23388545, PMID 23945234, PMID 34717557, PMID 39071816.

Gene Expression Profiling of Ulcerative Colitis

Select

Organization: University of Ulsan College of Medicine

Case ulcerative colitis Control normal 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: Ulcerative colitis.
Processed data is available for downstream review.

warning Total sample count is below the minimum needed for two comparison groups. 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.

Inflammation, adenoma and cancer: objective classification of colon biopsy specimens with gene expression signature

Select

Organization: Hungarian Academy of Sciences

Case colorectal cancer Control normal tissue

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: Colorectal cancer, Crohn's disease, Inflammatory bowel disease, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: Expression Atlas curated experiment link is available.
External evidence: PubMed links 12 publications; 12 DOIs available: PMID 18776587, PMID 19461970, PMID 20957034, PMID 23155391, PMID 25405986.

Expression data in colon mucosa samples from individuals with ulcerative colitis and normal controls

Select

Organization: Baylor College of Medicine

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 24937444.

Effects of Inflammation and 5-ASA on ex vivo cultured ulcerative colitis biopsies

Select

Organization: Queen Mary University

Case inflamed tissue Control non-inflamed tissue

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.

Transcriptional analysis of left-sided colitis, pancolitis and ulcerative colitis-associated dysplasia

Select

Organization: Herlev Hospital

Case mixed disease cohort 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: PubMed links 17 publications; 17 DOIs available: PMID 25358065, PMID 33987007, PMID 35604388, PMID 36982725, PMID 37056910.

Mucosal gene expression profiling in (un)inflamed colon of patients with ulcerative colitis (UC)

Select

Organization: KU Leuven

Case inflamed tissue 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: PubMed links 12 publications; 11 DOIs available: PMID 25546151, PMID 33144895, PMID 33462173, PMID 33941565, PMID 34939750.

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.