GSE215924

Small bowel RNA-seq data from patients with Crohn's disease and patients with colon cancer (non-CD controls)

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

70 case / 9 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.

Summary

To identify the dysregulated molecular pathways and core genes associated with the chronic and progressive course of CD, we evaluated the gene expression profiles of uninflamed small bowel tissues from CD patients who underwent small bowel resection and compared the results with those of patients with right colon cancer, who served as uninflamed non-CD controls.

Overall design

Comparative gene expression profiling analysis of RNA-seq data for patients with CD and non-CD controls. ***submitter declares that the raw data can not provided due to patient privacy concerns/hospital policy***

Source Evidence

4 sources
Source Contribution Status
GEO

Original dataset metadata, sample metadata, source links, and GEO data availability flags.

Sample records
79 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

Publication context when PubMed identifiers are already known.

No match found

Metadata Quality Components

Analysis Readiness

Ready after review
97% DE readiness

Contrast completeness

25/25 pts

Both case and control groups are present in the proposed grouping.

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

15/15 pts

All samples are assigned to a case or control group.

Blocking warnings

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

No readiness blockers detected.

Next Steps

  • Verify the proposed sample assignments and case-versus-control comparison against the GEO metadata before using them in DESeq2 or another differential-expression tool.
  • Confirm processed count files and sample identifiers match the exported metadata.

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

Siftome proposed case and control labels, but no reviewer confirmation is stored yet.

Open the sample grouping CSV and confirm group labels before analysis.

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

Confirm whether the cohort is large enough for the intended statistical analysis.

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

Ready

No review-needed or unassigned samples are present in the proposed grouping.

Review the grouping table for biologically meaningful differences that the automated checks may not detect.

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

Standard analyst review

Proceed only after the analyst confirms grouping, exclusions, and source files.

By Siftome standards, no expert review was triggered.

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

  • Disease context Crohn's disease, colorectal cancer Disease context came from Normalization rules.
  • Likely case group Crohn's disease 70 samples
  • Likely control group Control 9 samples

Ranking Facts

Supporting evidence

  • Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Interpreted disease metadata: Colorectal cancer, Crohn's disease.
  • Processed data is available for downstream review.

Cautions

  • Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Normalized Fields

251 fields

Sample Group Preview

showing 59 of 79 preview rows
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Study totals: Case 70 | Control 9 | Unassigned 0 | Excluded 0 | Ambiguous 0 showing 59 of 79 preview rows
Group Role Accession Title Source / characteristics Reason
Crohn's disease Case GSM6647498 CD03, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647499 CD04, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647500 CD05, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647501 CD06, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647502 CD07, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647503 CD08, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647504 CD09, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647505 CD10, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647506 CD11, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647507 CD12, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647508 CD14, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647509 CD15, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647510 CD16, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647511 CD17, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647512 CD18, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647513 CD19, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647514 CD20, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647515 CD21, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647516 CD22, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647517 CD23, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647518 CD24, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647519 CD25, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647520 CD26, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647521 CD27, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647522 CD28, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647523 CD29, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647524 CD30, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647525 CD31, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647526 CD32, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647527 CD33, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647528 CD34, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647529 CD35, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647530 CD36, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647531 CD37, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647532 CD38, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647533 CD39, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647534 CD40, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647535 CD41, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647536 CD42, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647537 CD44, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647538 CD45, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647539 CD46, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647540 CD48, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647541 CD49, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647542 CD50, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647543 CD51, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647544 CD52, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647545 CD54, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647546 CD56, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM6647547 CD57, CD participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Crohn's disease Case marker detected.
20 additional case samples are hidden from this preview.
Control Control GSM6647568 Non_CD01, Control participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Colon cancer Sample-local control marker detected.
Control Control GSM6647569 Non_CD02, Control participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Colon cancer Sample-local control marker detected.
Control Control GSM6647570 Non_CD03, Control participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Colon cancer Sample-local control marker detected.
Control Control GSM6647571 Non_CD04, Control participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Colon cancer Sample-local control marker detected.
Control Control GSM6647572 Non_CD05, Control participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Colon cancer Sample-local control marker detected.
Control Control GSM6647573 Non_CD06, Control participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Colon cancer Sample-local control marker detected.
Control Control GSM6647574 Non_CD07, Control participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Colon cancer Sample-local control marker detected.
Control Control GSM6647575 Non_CD08, Control participants, Ileum tissue Ileum Tissue: Ileum; Sex: Male; Disease state: Colon cancer Sample-local control marker detected.
Control Control GSM6647576 Non_CD09, Control participants, Ileum tissue Ileum Tissue: Ileum; Sex: Female; Disease state: Colon cancer Sample-local 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.