GSE72780

Intestinal epithelial cells from Crohn's Disease patients

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

5 case / 4 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
9 samples
Specimen
Tissue
Reported/interpreted study design
Disease/model vs control Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Günther C, Vetrano S, Danese S, Becker C, López Posadas R
Contact name
Rocío López Posadas
Submission date
2015-09-08
Last update
2019-03-25
Organization
University of Erlangen-Nuremberg
Department
Medicine Clinic 1
Public date
2015-12-01
Experiment types
Expression profiling by array
Platforms
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Series type
Series
SubSeries
Not available
BioProject
PRJNA295053

Summary

Inflammatory Bowel Diseases are associated with marked alterations of IECs with a subsequent loss of barrier function. To identify alterations in signaling pathways in intestinal epithelium upon inflammation, we analyzed the transcriptome of IECs from patients suffering from Crohn’s disease.

Overall design

Intestinal epithelial cells were isolated from the terminal ileum of Crohn´s Disease patients (4 uninflamed and 5 inflamed areas). RNA was isolated and subjected to Affymetrix gene chip analysis

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
9 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. Rho-A prenylation and signaling link epithelial homeostasis to intestinal inflammation. The Journal of clinical investigation, 2016
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
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

Bioinformatician review required

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

Assay context may require expert handling before DESeq2-style 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 Disease context came from Normalization rules.
  • Likely case group Inflamed tissue 5 samples
  • Likely control group Non-inflamed tissue 4 samples

Intent Interpretation

  • Downgrade or exclusion reason Downgraded assay: microarray cohorts are separated from the RNA-seq intent. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

  • Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%.
  • 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 26752649.
  • Publication context: Rho-A prenylation and signaling link epithelial homeostasis to intestinal inflammation.. The Journal of clinical investigation, 2016. PMID 26752649. DOI 10.1172/JCI80997.

Cautions

  • Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
  • Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
  • Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because fewer than ten samples limit cohort confidence.
  • Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Normalized Fields

37 fields

Sample Group Preview

9 rows shown Show Hide
Study totals: Case 5 | Control 4 | Unassigned 0 | Excluded 0 | Ambiguous 0 9 rows shown
Group Role Accession Title Source / characteristics Reason
Inflamed tissue Case GSM1871908 Inflamed, biological rep1 Intestinal Epithelial Cells (IECs) from Crohn´s Disease (CD) patient Tissue: Intestinal Epitehlial Cells (terminal ileum) Case marker detected.
Inflamed tissue Case GSM1871909 Inflamed, biological rep2 Intestinal Epithelial Cells (IECs) from Crohn´s Disease (CD) patient Tissue: Intestinal Epitehlial Cells (terminal ileum) Case marker detected.
Inflamed tissue Case GSM1871910 Inflamed, biological rep3 Intestinal Epithelial Cells (IECs) from Crohn´s Disease (CD) patient Tissue: Intestinal Epitehlial Cells (terminal ileum) Case marker detected.
Inflamed tissue Case GSM1871911 Inflamed, biological rep4 Intestinal Epithelial Cells (IECs) from Crohn´s Disease (CD) patient Tissue: Intestinal Epitehlial Cells (terminal ileum) Case marker detected.
Inflamed tissue Case GSM1871912 Inflamed, biological rep5 Intestinal Epithelial Cells (IECs) from Crohn´s Disease (CD) patient Tissue: Intestinal Epitehlial Cells (terminal ileum) Case marker detected.
Non-inflamed tissue Control GSM1871904 Uninflamed, biological rep1 Intestinal Epithelial Cells (IECs) from Healthy patient Tissue: Intestinal Epitehlial Cells (terminal ileum) Sample-local control marker detected.
Non-inflamed tissue Control GSM1871905 Uninflamed, biological rep2 Intestinal Epithelial Cells (IECs) from Healthy patient Tissue: Intestinal Epitehlial Cells (terminal ileum) Sample-local control marker detected.
Non-inflamed tissue Control GSM1871906 Uninflamed, biological rep3 Intestinal Epithelial Cells (IECs) from Healthy patient Tissue: Intestinal Epitehlial Cells (terminal ileum) Sample-local control marker detected.
Non-inflamed tissue Control GSM1871907 Uninflamed, biological rep4 Intestinal Epithelial Cells (IECs) from Healthy patient Tissue: Intestinal Epitehlial Cells (terminal ileum) 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.