GSE208303

RNA-seq for inflamed and non-inflamed mucosa in patients with Crohn's disease

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

13 case / 22 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
bulk RNA-seq
Organism
Homo sapiens
Whole-study samples
35 samples
Specimen
Tissue
Reported/interpreted study design
Disease/model vs control Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Hong SN, Lee C, Joung J, Hong S
Contact name
Sung Noh Hong
Submission date
2022-07-15
Last update
2022-08-31
Organization
Samsung Medical Center
Department
Gastroenterolgy
Public date
2022-07-19
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA859159

Summary

To investigate the gene expression profile of inflamed and non-inflamed mucosa in patients with Crohn's disease. To investigate TCR repertoires in the intestinal mucosa, the expression profile of the TCR repertoire gene was analyzed.

Overall design

We prospectively enrolled 13 patients with active CD (mean age: 30.9 ± 10.9 years; 9 were males) who underwent diagnostic or surveillance colonoscopy. Clinical characteristics of the enrolled patients were as follows: Montreal classification A1 / A2 / A3, n = 2 / n = 8 / n = 3; L1 / L2 / L3, n = 6 / n = 2 / n = 5; B1 / B2 / B3, n = 5 / n = 5 / n = 3. During colonoscopy, 2-4 biopsy samples were taken from active ulcer margins (inflamed intestinal mucosa, n = 13) and endoscopically normal-appearing mucosa (non-inflamed intestinal mucosa, n = 13) from each patient with CD. As controls, 9 non-IBD patients were enrolled prospectively (mean age: 49.7 ± 14.9 years; 6 were males) who underwent colonoscopies for colorectal polyp removal. Endoscopically normal-appearing healthy colonic mucosa specimens were obtained from the ascending colon of each non-IBD control (healthy mucosa of non-IBD control, n = 9). *** Submitter declares that institutional policy restricts the deposit of patient raw data outside the institution. ***

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
35 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

  1. Reduced diversity of intestinal T-cell receptor repertoire in patients with Crohn's disease. Frontiers in cellular and infection microbiology, 2022
Available

Metadata Quality Components

Persisted metadata quality

100 pts
Clarity
100%
Weight
100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. 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

Ready after review
100% 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

10/10 pts

No dataset warnings are present.

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, inflammatory bowel disease Disease context came from Normalization rules.
  • Likely case group Inflamed tissue 13 samples
  • Likely control group Non-inflamed tissue 22 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: Crohn's disease, Inflammatory bowel disease.
  • Processed data is available for downstream review.
  • External evidence: PubMed links 1 publication; 1 DOI available: PMID 36034703.
  • Publication context: Reduced diversity of intestinal T-cell receptor repertoire in patients with Crohn's disease.. Frontiers in cellular and infection microbiology, 2022. PMID 36034703. DOI 10.3389/fcimb.2022.932373.

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.
  • Publication context: Reduced diversity of intestinal T-cell receptor repertoire in patients with Crohn's disease.. Frontiers in cellular and infection microbiology, 2022. PMID 36034703. DOI 10.3389/fcimb.2022.932373.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

No dataset warnings

Normalized Fields

93 fields

Sample Group Preview

35 rows shown Show Hide
Study totals: Case 13 | Control 22 | Unassigned 0 | Excluded 0 | Ambiguous 0 35 rows shown
Group Role Accession Title Source / characteristics Reason
Inflamed tissue Case GSM6340480 Inflamed mucosa of CD #1 Inflamed mucosa Disease state: Crohn's disease; Individual id: CD #1; Tissue: Inflamed mucosa Explicit sample label case marker detected.
Inflamed tissue Case GSM6340482 Inflamed mucosa of CD #2 Inflamed mucosa Disease state: Crohn's disease; Individual id: CD #2; Tissue: Inflamed mucosa Explicit sample label case marker detected.
Inflamed tissue Case GSM6340484 Inflamed mucosa of CD #3 Inflamed mucosa Disease state: Crohn's disease; Individual id: CD #3; Tissue: Inflamed mucosa Explicit sample label case marker detected.
Inflamed tissue Case GSM6340486 Inflamed mucosa of CD #4 Inflamed mucosa Disease state: Crohn's disease; Individual id: CD #4; Tissue: Inflamed mucosa Explicit sample label case marker detected.
Inflamed tissue Case GSM6340488 Inflamed mucosa of CD #5 Inflamed mucosa Disease state: Crohn's disease; Individual id: CD #5; Tissue: Inflamed mucosa Explicit sample label case marker detected.
Inflamed tissue Case GSM6340490 Inflamed mucosa of CD #6 Inflamed mucosa Disease state: Crohn's disease; Individual id: CD #6; Tissue: Inflamed mucosa Explicit sample label case marker detected.
Inflamed tissue Case GSM6340492 Inflamed mucosa of CD #7 Inflamed mucosa Disease state: Crohn's disease; Individual id: CD #7; Tissue: Inflamed mucosa Explicit sample label case marker detected.
Inflamed tissue Case GSM6340494 Inflamed mucosa of CD #8 Inflamed mucosa Disease state: Crohn's disease; Individual id: CD #8; Tissue: Inflamed mucosa Explicit sample label case marker detected.
Inflamed tissue Case GSM6340496 Inflamed mucosa of CD #9 Inflamed mucosa Disease state: Crohn's disease; Individual id: CD #9; Tissue: Inflamed mucosa Explicit sample label case marker detected.
Inflamed tissue Case GSM6340498 Inflamed mucosa of CD #10 Inflamed mucosa Disease state: Crohn's disease; Individual id: CD #10; Tissue: Inflamed mucosa Explicit sample label case marker detected.
Inflamed tissue Case GSM6340500 Inflamed mucosa of CD #11 Inflamed mucosa Disease state: Crohn's disease; Individual id: CD #11; Tissue: Inflamed mucosa Explicit sample label case marker detected.
Inflamed tissue Case GSM6340502 Inflamed mucosa of CD #12 Inflamed mucosa Disease state: Crohn's disease; Individual id: CD #12; Tissue: Inflamed mucosa Explicit sample label case marker detected.
Inflamed tissue Case GSM6340504 Inflamed mucosa of CD #13 Inflamed mucosa Disease state: Crohn's disease; Individual id: CD #13; Tissue: Inflamed mucosa Explicit sample label case marker detected.
Non-inflamed tissue Control GSM6340481 Non-inflamed mucosa of CD #1 Non-inflamed mucosa Disease state: Crohn's disease; Individual id: CD #1; Tissue: Non-inflamed mucosa Sample-local control marker detected.
Non-inflamed tissue Control GSM6340483 Non-inflamed mucosa of CD #2 Non-inflamed mucosa Disease state: Crohn's disease; Individual id: CD #2; Tissue: Non-inflamed mucosa Sample-local control marker detected.
Non-inflamed tissue Control GSM6340485 Non-inflamed mucosa of CD #3 Non-inflamed mucosa Disease state: Crohn's disease; Individual id: CD #3; Tissue: Non-inflamed mucosa Sample-local control marker detected.
Non-inflamed tissue Control GSM6340487 Non-inflamed mucosa of CD #4 Non-inflamed mucosa Disease state: Crohn's disease; Individual id: CD #4; Tissue: Non-inflamed mucosa Sample-local control marker detected.
Non-inflamed tissue Control GSM6340489 Non-inflamed mucosa of CD #5 Non-inflamed mucosa Disease state: Crohn's disease; Individual id: CD #5; Tissue: Non-inflamed mucosa Sample-local control marker detected.
Non-inflamed tissue Control GSM6340491 Non-inflamed mucosa of CD #6 Non-inflamed mucosa Disease state: Crohn's disease; Individual id: CD #6; Tissue: Non-inflamed mucosa Sample-local control marker detected.
Non-inflamed tissue Control GSM6340493 Non-inflamed mucosa of CD #7 Non-inflamed mucosa Disease state: Crohn's disease; Individual id: CD #7; Tissue: Non-inflamed mucosa Sample-local control marker detected.
Non-inflamed tissue Control GSM6340495 Non-inflamed mucosa of CD #8 Non-inflamed mucosa Disease state: Crohn's disease; Individual id: CD #8; Tissue: Non-inflamed mucosa Sample-local control marker detected.
Non-inflamed tissue Control GSM6340497 Non-inflamed mucosa of CD #9 Non-inflamed mucosa Disease state: Crohn's disease; Individual id: CD #9; Tissue: Non-inflamed mucosa Sample-local control marker detected.
Non-inflamed tissue Control GSM6340499 Non-inflamed mucosa of CD #10 Non-inflamed mucosa Disease state: Crohn's disease; Individual id: CD #10; Tissue: Non-inflamed mucosa Sample-local control marker detected.
Non-inflamed tissue Control GSM6340501 Non-inflamed mucosa of CD #11 Non-inflamed mucosa Disease state: Crohn's disease; Individual id: CD #11; Tissue: Non-inflamed mucosa Sample-local control marker detected.
Non-inflamed tissue Control GSM6340503 Non-inflamed mucosa of CD #12 Non-inflamed mucosa Disease state: Crohn's disease; Individual id: CD #12; Tissue: Non-inflamed mucosa Sample-local control marker detected.
Non-inflamed tissue Control GSM6340505 Non-inflamed mucosa of CD #13 Non-inflamed mucosa Disease state: Crohn's disease; Individual id: CD #13; Tissue: Non-inflamed mucosa Sample-local control marker detected.
Control Control GSM6340506 Healthy mucosa of non-IBD control #1 Healthy mucosa Disease state: Control; Individual id: Control #1; Tissue: Healthy mucosa Sample-local control marker detected.
Control Control GSM6340507 Healthy mucosa of non-IBD control #2 Healthy mucosa Disease state: Control; Individual id: Control #2; Tissue: Healthy mucosa Sample-local control marker detected.
Control Control GSM6340508 Healthy mucosa of non-IBD control #3 Healthy mucosa Disease state: Control; Individual id: Control #3; Tissue: Healthy mucosa Sample-local control marker detected.
Control Control GSM6340509 Healthy mucosa of non-IBD control #4 Healthy mucosa Disease state: Control; Individual id: Control #4; Tissue: Healthy mucosa Sample-local control marker detected.
Control Control GSM6340510 Healthy mucosa of non-IBD control #5 Healthy mucosa Disease state: Control; Individual id: Control #5; Tissue: Healthy mucosa Sample-local control marker detected.
Control Control GSM6340511 Healthy mucosa of non-IBD control #6 Healthy mucosa Disease state: Control; Individual id: Control #6; Tissue: Healthy mucosa Sample-local control marker detected.
Control Control GSM6340512 Healthy mucosa of non-IBD control #7 Healthy mucosa Disease state: Control; Individual id: Control #7; Tissue: Healthy mucosa Sample-local control marker detected.
Control Control GSM6340513 Healthy mucosa of non-IBD control #8 Healthy mucosa Disease state: Control; Individual id: Control #8; Tissue: Healthy mucosa Sample-local control marker detected.
Control Control GSM6340514 Healthy mucosa of non-IBD control #9 Healthy mucosa Disease state: Control; Individual id: Control #9; Tissue: Healthy mucosa 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.