GSE77013

A long noncoding RNA signature in Ulcerative Colitis

Whole-study status Not suitable

Dataset does not meet the current suitability threshold.

Whole-study downloads — these do not apply your sample requirements.

Selected cohort requirements

Samples meeting selected requirements: 0 cases / 0 controls

View matching samples

12 case / 0 control samples elsewhere in the study have incomplete or conflicting evidence; they are not included above

Patient pairs verified in indexed sample metadata: 0

A case/control comparison meeting these requirements is not confirmed.

Counts describe samples, not independent patients. Pair verification uses explicit subject identifiers in indexed sample metadata. Zero verified pairs does not establish that the study is unpaired; reported matched-normal design alone is insufficient.

Source: GEO
Assay: microarray
Organism: Homo sapiens
Whole-study samples: 19 samples
Specimen: Tissue
Reported/interpreted study design: Unclear study design Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Padua DM, Iliopoulos D
Contact name: David Miguel Padua
Submission date: 2016-01-20
Last update: 2018-03-12
Organization: UCLA
Department: Medicine-Division of Digestive Diseases
Public date: 2016-11-08
Experiment types: Non-coding RNA profiling by array
Platforms: GPL16956 Agilent-045997 Arraystar human lncRNA microarray V3 (Probe Name Version)
Series type: Series
SubSeries: Not available
BioProject: PRJNA309287

Summary

Background & Aims: Inflammatory bowel diseases (IBD) are clinically manifested as ulcerative colitis (UC) and Crohn’s Disease (CD). Novel high throughput technologies revealed new categories of genes, including the long non-coding RNAs (lncRNAs), which have been involved in the pathogenesis of different human diseases; however the role and function of lncRNAs in the UC pathogenesis has not been evaluated. Methods: The gene expression patterns for both non-coding (lncRNAs) and coding (mRNA) transcripts were profiled in UC (n=8) and control (n=7) patients by ArrayStar assays. The differentially expressed genes were used to develop lncRNA signatures in UC samples. Ingenuity Software Analysis (IPA) program was used to identify the up-stream regulators of IFNG-AS1. Jurkat T cells were activated by PMA/ionomycin and IFNG and TNF protein levels were assessed by ELISA assay. Two anti-sense molecules were designed and used to block IFNG-AS1 expression levels. Colonic tissues from TNBS-treated and IL10-/- mice were used to extract RNA and examine INFG-AS1 expression by real-time PCR. Results: A unique set of lncRNAs was found to be differentially expressed between UC (n=15) and control samples (n=16). Of these, IFNG-AS1 was among the highest statistically significant lncRNAs (fold change: 5.27, p-value: 7.07E-06). Bioinformatic analyses showed that IFNG-AS1 was associated with the IBD susceptibility loci SNP rs7134599 and its genomic location is adjacent to the inflammatory cytokine, interferon-gamma (IFNG). Using the TNBS and IL10-/- mouse models of colitis, we found increased colonic expression of this lncRNA during active colitis. Utilizing the Jurkat T cell model system, we explored the mechanisms of action and found that IFNG-AS1 can positively regulate IFNG expression. Conclusions: Novel lncRNA signatures were identified to differentiate UC patients with active disease, in remission and control subjects. A subset of these lncRNAs was found to be associated with the clinically validated IBD susceptibility loci. IFNG-AS1 was one of these differentially expressed lncRNAs in UC patients and was found to regulate the key inflammatory cytokine, IFNG, in CD4 T cells. Taken together, our study revealed novel lncRNA signatures deregulated in ulcerative colitis and identified IFNG-AS1 as a novel regulator of IFNG inflammatory responses, suggesting the potential importance of non-coding RNA mechanisms on regulation of IBD-related inflammatory responses.

Overall design

19 overall samples were analyzed. Colonic resection samples from 8 Active Ulcerative colitis, 4 Inactive Ulcerative colitis, 7 control samples

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 19 GSM samples	Primary source
recount3	Planned trusted source for processed count availability.	No match found
Expression Atlas	Planned source for curated expression experiment links.	No match found
PubMed	Primary GEO citations and related PubMed articles that mention this dataset. 1 linked publication 1 DOI Primary publication A long noncoding RNA signature for ulcerative colitis identifies IFNG-AS1 as an enhancer of inflammation. American journal of physiology. Gastrointestinal and liver physiology, 2016 PubMed DOI	Available

Metadata Quality Components

Persisted metadata quality

93 pts

Clarity: 93%
Weight: 100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Only one side of the comparison is clearly grouped. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Anatomical source metadata normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Analysis Readiness

Not ready

43% DE readiness

Contrast completeness

10/25 pts

Only one side of the contrast is present; downstream DE needs both groups.

Minimum group size

0/20 pts

Minimum group size cannot be evaluated until a complete contrast exists.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

3/15 pts

Unassigned or review-needed samples remain before analysis.

Blocking warnings

0/10 pts

Critical warnings must be resolved before downstream analysis.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

No complete case/control contrast is available.
7 samples are still unassigned.
Critical dataset warnings must be resolved.
Secondary RNA assay context should be analyzed separately from ordinary bulk RNA-seq.

Next Steps

Resolve unassigned or review-needed samples in the grouping table.
Resolve critical warnings before downstream analysis.

Analysis Preparation Checklist

3/6 ready

Group labels reviewed

Blocked

No complete case/control grouping exists yet.

Review the sample grouping table and assign both case and control groups.

Minimum sample count met

Blocked

At least one group has fewer than 2 samples.

Choose a larger dataset or merge only scientifically valid groups.

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

Verify that downloaded processed files contain usable count or expression identifiers.

Ambiguous samples handled

Needs review

0 review-needed samples and 7 unassigned samples remain.

Resolve ambiguous and unassigned samples before finalizing the contrast.

Exclusion decisions recorded

Ready

No hard-excluded samples were detected by the current rules.

Record any manual exclusions in the downstream analysis notes.

Source traceability preserved

Ready

The dataset and sample accessions can be traced back to GEO.

Keep GEO accessions with exported metadata.

Bioinformatician Review

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.

Analysis readiness has blockers that must be resolved before DE.

Analysis preparation checklist contains blocked items.

No complete case/control or treatment/control contrast is available.

At least one comparison group has fewer than two samples.

One or more samples are unassigned and need manual grouping decisions.

Critical dataset warnings are present.

Assay context may require expert handling before DESeq2-style analysis.

Study design is model-system or unclear and should be reviewed before analysis.

Why This Is Ranked Here

Tumor vs normal

Not suitable Dataset does not meet the current suitability threshold.

Applied Review Decisions

No active review decisions affect this ranking.

Derived Classifications

Assay differs from search intent Microarray Search intent expects bulk RNA-seq. Assay came from Normalization rules.
Disease context Crohn's disease, inflammatory bowel disease, ulcerative colitis Disease context came from Normalization rules.
Likely case group Ulcerative colitis 12 samples
Likely control group No control group detected 0 samples

Intent Interpretation

Downgrade or exclusion reason Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

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 27492330.
Publication context: A long noncoding RNA signature for ulcerative colitis identifies IFNG-AS1 as an enhancer of inflammation.. American journal of physiology. Gastrointestinal and liver physiology, 2016. PMID 27492330. DOI 10.1152/ajpgi.00212.2016.

Cautions

Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%.
Downgraded for tissue search because study design or specimen source is unclear.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
Overall score capped because comparison suitability is weak for the selected search intent.
Missing or unclear metadata. Comparison - Unclear study design. Specimen - Tissue. Comparison suitability: 0%.
Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

No clear control group was detected from normalized metadata.
Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
Microarray expression context was detected; compare separately from RNA-seq cohorts.
Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Normalized Fields

57 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source colon GSM2042464 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Colon tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2042465 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Colon tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2042466 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Colon tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2042467 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Colon tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2042468 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Colon tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2042469 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Colon tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2042470 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Colon tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2042471 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Colon tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2042472 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Colon tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2042473 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Colon tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2042474 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Colon tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2042475 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Colon tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2042476 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Colon tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2042477 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Colon tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2042478 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Colon tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2042479 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Colon tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2042480 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Colon tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2042481 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Colon tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2042482 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Colon tissue sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE77013 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE77013 dataset_title: A long noncoding RNA signature in Ulcerative Colitis organism: Homo sapiens assay_type: microarray processed_data_available: true raw_... keyword match keyword match: microarray

disease Crohn's disease GSE77013 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease dataset_accession: GSE77013 dataset_title: A long noncoding RNA signature in Ulcerative Colitis organism: Homo sapiens assay_type: microarray processed_data_available: true raw_... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease inflammatory bowel disease GSE77013 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel dataset_accession: GSE77013 dataset_title: A long noncoding RNA signature in Ulcerative Colitis organism: Homo sapiens assay_type: microarray processed_data_available: true raw_... controlled vocabulary controlled vocabulary disease match: inflammatory bowel

disease ulcerative colitis GSE77013 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis dataset_accession: GSE77013 dataset_title: A long noncoding RNA signature in Ulcerative Colitis organism: Homo sapiens assay_type: microarray processed_data_available: true raw_... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2042471 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis UCA1 Colon tissue age: 30; gender: Female; location: colon; sample type: active ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2042472 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis UCA2 Colon tissue age: 56; gender: Female; location: colon:left; sample type: active ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2042473 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis UCA3 Colon tissue age: 26; gender: Female; location: colon; sample type: active ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2042474 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis UCA4 Colon tissue age: 46; gender: Female; location: colon; sample type: active ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2042475 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis UCA5 Colon tissue age: 29; gender: Male; location: colon; sample type: active ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2042476 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis UCA6 Colon tissue age: 24; gender: Male; location: colon; sample type: active ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2042477 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis UCA7 Colon tissue age: 45; gender: Female; location: colon; sample type: active ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2042478 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis UCA8 Colon tissue age: 26; gender: Female; location: colon; sample type: active ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2042479 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis UCI1 Colon tissue age: 31; gender: Male; location: colon; sample type: inactive ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2042480 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis UCI2 Colon tissue age: 71; gender: Female; location: colon; sample type: inactive ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2042481 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis UCI3 Colon tissue age: 51; gender: Male; location: colon; sample type: inactive ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2042482 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis UCI4 Colon tissue age: 33; gender: Female; location: colon; sample type: inactive ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

organism Homo sapiens GSE77013 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE77013 dataset_title: A long noncoding RNA signature in Ulcerative Colitis organism: Homo sapiens assay_type: microarray processed_data_available: true raw_... keyword match keyword match: homo sapiens

organism Mus musculus GSE77013 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence mouse dataset_accession: GSE77013 dataset_title: A long noncoding RNA signature in Ulcerative Colitis organism: Homo sapiens assay_type: microarray processed_data_available: true raw_... keyword match keyword match: mouse

tissue colon GSE77013 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colonic dataset_accession: GSE77013 dataset_title: A long noncoding RNA signature in Ulcerative Colitis organism: Homo sapiens assay_type: microarray processed_data_available: true raw_... controlled vocabulary controlled vocabulary tissue match: colonic

tissue colon GSM2042464 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Con1 Colon tissue age: 31; gender: Male; location: colon; sample type: control controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2042465 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Con2 Colon tissue age: 45; gender: Female; location: colon; sample type: control controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2042466 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Con3 Colon tissue age: 26; gender: Male; location: colon:sigmoid; sample type: control controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2042467 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Con4 Colon tissue age: 46; gender: Male; location: colon; sample type: control controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2042468 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Con5 Colon tissue age: 50; gender: Female; location: colon; sample type: control controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2042469 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Con6 Colon tissue age: 60; gender: Female; location: colon; sample type: control controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2042470 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Con7 Colon tissue age: 56; gender: Male; location: colon; sample type: control controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2042471 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UCA1 Colon tissue age: 30; gender: Female; location: colon; sample type: active ulcerative colitis controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2042472 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UCA2 Colon tissue age: 56; gender: Female; location: colon:left; sample type: active ulcerative colitis controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2042473 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UCA3 Colon tissue age: 26; gender: Female; location: colon; sample type: active ulcerative colitis controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2042474 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UCA4 Colon tissue age: 46; gender: Female; location: colon; sample type: active ulcerative colitis controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2042475 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UCA5 Colon tissue age: 29; gender: Male; location: colon; sample type: active ulcerative colitis controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2042476 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UCA6 Colon tissue age: 24; gender: Male; location: colon; sample type: active ulcerative colitis controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2042477 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UCA7 Colon tissue age: 45; gender: Female; location: colon; sample type: active ulcerative colitis controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2042478 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UCA8 Colon tissue age: 26; gender: Female; location: colon; sample type: active ulcerative colitis controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2042479 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UCI1 Colon tissue age: 31; gender: Male; location: colon; sample type: inactive ulcerative colitis controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2042480 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UCI2 Colon tissue age: 71; gender: Female; location: colon; sample type: inactive ulcerative colitis controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2042481 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UCI3 Colon tissue age: 51; gender: Male; location: colon; sample type: inactive ulcerative colitis controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2042482 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UCI4 Colon tissue age: 33; gender: Female; location: colon; sample type: inactive ulcerative colitis controlled vocabulary controlled vocabulary tissue match: colon

Sample Group Preview

19 rows shown Show Hide

Study totals: Case 12 | Control 0 | Unassigned 7 | Excluded 0 | Ambiguous 0 19 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Ulcerative colitis	Case	GSM2042471	UCA1	Colon tissue Age: 30; Gender: Female; Location: Colon; Sample type: Active ulcerative colitis	Case marker detected.
Ulcerative colitis	Case	GSM2042472	UCA2	Colon tissue Age: 56; Gender: Female; Location: Colon:Left; Sample type: Active ulcerative colitis	Case marker detected.
Ulcerative colitis	Case	GSM2042473	UCA3	Colon tissue Age: 26; Gender: Female; Location: Colon; Sample type: Active ulcerative colitis	Case marker detected.
Ulcerative colitis	Case	GSM2042474	UCA4	Colon tissue Age: 46; Gender: Female; Location: Colon; Sample type: Active ulcerative colitis	Case marker detected.
Ulcerative colitis	Case	GSM2042475	UCA5	Colon tissue Age: 29; Gender: Male; Location: Colon; Sample type: Active ulcerative colitis	Case marker detected.
Ulcerative colitis	Case	GSM2042476	UCA6	Colon tissue Age: 24; Gender: Male; Location: Colon; Sample type: Active ulcerative colitis	Case marker detected.
Ulcerative colitis	Case	GSM2042477	UCA7	Colon tissue Age: 45; Gender: Female; Location: Colon; Sample type: Active ulcerative colitis	Case marker detected.
Ulcerative colitis	Case	GSM2042478	UCA8	Colon tissue Age: 26; Gender: Female; Location: Colon; Sample type: Active ulcerative colitis	Case marker detected.
Ulcerative colitis	Case	GSM2042479	UCI1	Colon tissue Age: 31; Gender: Male; Location: Colon; Sample type: Inactive ulcerative colitis	Case marker detected.
Ulcerative colitis	Case	GSM2042480	UCI2	Colon tissue Age: 71; Gender: Female; Location: Colon; Sample type: Inactive ulcerative colitis	Case marker detected.
Ulcerative colitis	Case	GSM2042481	UCI3	Colon tissue Age: 51; Gender: Male; Location: Colon; Sample type: Inactive ulcerative colitis	Case marker detected.
Ulcerative colitis	Case	GSM2042482	UCI4	Colon tissue Age: 33; Gender: Female; Location: Colon; Sample type: Inactive ulcerative colitis	Case marker detected.
Unassigned	Unassigned	GSM2042464	Con1	Colon tissue Age: 31; Gender: Male; Location: Colon; Sample type: Control	No explicit case or control marker detected.
Unassigned	Unassigned	GSM2042465	Con2	Colon tissue Age: 45; Gender: Female; Location: Colon; Sample type: Control	No explicit case or control marker detected.
Unassigned	Unassigned	GSM2042466	Con3	Colon tissue Age: 26; Gender: Male; Location: Colon:Sigmoid; Sample type: Control	No explicit case or control marker detected.
Unassigned	Unassigned	GSM2042467	Con4	Colon tissue Age: 46; Gender: Male; Location: Colon; Sample type: Control	No explicit case or control marker detected.
Unassigned	Unassigned	GSM2042468	Con5	Colon tissue Age: 50; Gender: Female; Location: Colon; Sample type: Control	No explicit case or control marker detected.
Unassigned	Unassigned	GSM2042469	Con6	Colon tissue Age: 60; Gender: Female; Location: Colon; Sample type: Control	No explicit case or control marker detected.
Unassigned	Unassigned	GSM2042470	Con7	Colon tissue Age: 56; Gender: Male; Location: Colon; Sample type: Control	No explicit case or control marker detected.

Use as Discovery Cohort

External Validation Finder

Carry Siftome's disease, organism, specimen, assay, data type, and accession into a validation project. Uncertain fields remain Unknown.

Summary

Overall design

Source Evidence

Primary publication

Metadata Quality Components

Analysis Readiness

Blockers

Next Steps

Analysis Preparation Checklist

Bioinformatician Review

Why This Is Ranked Here

Applied Review Decisions

Derived Classifications

Intent Interpretation

Ranking Facts

Supporting evidence

Cautions

Dataset Warnings

Normalized Fields

Sample Group Preview

Use as Discovery Cohort