GSE156044

Transcriptomics analysis of mesenteric adipose tissue from Crohn's disease patients and healthy controls [RNA-seq]

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

4 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
bulk RNA-seq
Organism
Homo sapiens
Whole-study samples
8 samples
Specimen
Tissue
Reported/interpreted study design
Unclear study design Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Ha CW, Devkota S, Wang Y, Core A
Contact name
AGCT Core
Submission date
2020-08-11
Last update
2021-10-19
Organization
Cedars Sinai Medical Center
Department
BMS
Public date
2020-08-28
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA656537

Summary

A feature of Crohn's disease is the extra-intestinal manifestation of creeping fat, defined as expansion of mesenteric adipose tissue around the inflamed and fibrotic ileum. In comparison to healthy controls, we found that the greatest transcriptional changes in creeping fat are functions related to immune response to bacterial products.

Overall design

We compared the transcriptional activity of creeping fat from four Crohn's disease patients and healthy mesenteric adipose tissues from ileal controls (IRB# Pro00048577).

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
8 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. Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans. Cell, 2020
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.
  • 4 samples are still unassigned.
  • Critical dataset warnings must be resolved.

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 4 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.

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

  • Disease context Crohn's disease, fibrosis Disease context came from Normalization rules.
  • Likely case group Crohn's disease 4 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

  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Interpreted disease metadata: Crohn's disease, Fibrosis.
  • Processed data is available for downstream review.
  • External evidence: PubMed links 1 publication; 1 DOI available: PMID 32991841.
  • Publication context: Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans.. Cell, 2020. PMID 32991841. DOI 10.1016/j.cell.2020.09.009.

Cautions

  • Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%.
  • Downgraded for tissue search because study design or specimen source is unclear.
  • 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.
  • Overall score capped because fewer than ten samples limit cohort confidence.
  • 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

Normalized Fields

13 fields

Sample Group Preview

8 rows shown Show Hide
Study totals: Case 4 | Control 0 | Unassigned 4 | Excluded 0 | Ambiguous 0 8 rows shown
Group Role Accession Title Source / characteristics Reason
Crohn's disease Case GSM4721214 CrF 1 Mesenteric adipose tissue Tissue: Creeping fat; Cohort: Crohn's disease Case marker detected.
Crohn's disease Case GSM4721215 CrF 2 Mesenteric adipose tissue Tissue: Creeping fat; Cohort: Crohn's disease Case marker detected.
Crohn's disease Case GSM4721216 CrF 3 Mesenteric adipose tissue Tissue: Creeping fat; Cohort: Crohn's disease Case marker detected.
Crohn's disease Case GSM4721217 CrF 4 Mesenteric adipose tissue Tissue: Creeping fat; Cohort: Crohn's disease Case marker detected.
Unassigned Unassigned GSM4721218 H-MAT 1 Mesenteric adipose tissue Tissue: Healthy mesenteric fat; Cohort: Healthy ileal controls No explicit case or control marker detected.
Unassigned Unassigned GSM4721219 H-MAT 2 Mesenteric adipose tissue Tissue: Healthy mesenteric fat; Cohort: Healthy ileal controls No explicit case or control marker detected.
Unassigned Unassigned GSM4721220 H-MAT 3 Mesenteric adipose tissue Tissue: Healthy mesenteric fat; Cohort: Healthy ileal controls No explicit case or control marker detected.
Unassigned Unassigned GSM4721221 H-MAT 4 Mesenteric adipose tissue Tissue: Healthy mesenteric fat; Cohort: Healthy ileal controls 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.