GSE102524

Inflammatory Bowel Disease-specific alterations in adipose-derived stroma cell transcriptional profiles

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

24 case / 6 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: 30 samples
Specimen: Tissue
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Karagiannides I, Hoffman JM, Karagiannidis I
Contact name: Iordanis Karagiannidis
Submission date: 2017-08-11
Last update: 2021-07-25
Organization: UCLA, David Geffen School of Medicine
Department: Not available
Public date: 2018-03-01
Experiment types: Expression profiling by array
Platforms: GPL16956 Agilent-045997 Arraystar human lncRNA microarray V3 (Probe Name Version)
Series type: Series
SubSeries: Not available
BioProject: PRJNA397972

Summary

Transcriptional profiling of primary human mesenteric adipose-derived stroma cells isolated from control, cancer, Crohn's disease, Ulcerative colitis, and obese patients

Overall design

five-condition experiment (see summary), 6 Biological replicates per group

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 30 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

Persisted metadata quality

85 pts

Clarity: 85%
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: Tissue metadata was not 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, ulcerative colitis Disease context came from Normalization rules.
Likely case group Cancer 24 samples
Likely control group Control 6 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, Ulcerative colitis.
Processed data is available for downstream review.

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.
Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
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

Microarray expression context was detected; compare separately from RNA-seq cohorts.
Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.

Normalized Fields

17 fields

Field Value Source Derived by Confidence Evidence Reason

assay_type microarray GSE102524 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE102524 dataset_title: Inflammatory Bowel Disease-specific alterations in adipose-derived stroma cell transcriptional profiles organism: Homo sapiens assay_... keyword match keyword match: microarray

disease Crohn's disease GSE102524 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease dataset_accession: GSE102524 dataset_title: Inflammatory Bowel Disease-specific alterations in adipose-derived stroma cell transcriptional profiles organism: Homo sapiens assay_... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease inflammatory bowel disease GSE102524 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease dataset_accession: GSE102524 dataset_title: Inflammatory Bowel Disease-specific alterations in adipose-derived stroma cell transcriptional profiles organism: Homo sapiens assay_... controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease ulcerative colitis GSE102524 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis dataset_accession: GSE102524 dataset_title: Inflammatory Bowel Disease-specific alterations in adipose-derived stroma cell transcriptional profiles organism: Homo sapiens assay_... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease Crohn's disease GSM2740121 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Crohn's Disease Adipose-derived Stroma Cell Replicate 1 Mesenteric Adipose-derived Stroma Cells disease: Crohn's Disease; passage: 4; cell type: Fibroblast-like precursors isola... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2740122 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Crohn's Disease Adipose-derived Stroma Cell Replicate 2 Mesenteric Adipose-derived Stroma Cells disease: Crohn's Disease; passage: 4; cell type: Fibroblast-like precursors isola... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2740123 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Crohn's Disease Adipose-derived Stroma Cell Replicate 3 Mesenteric Adipose-derived Stroma Cells disease: Crohn's Disease; passage: 4; cell type: Fibroblast-like precursors isola... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2740124 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Crohn's Disease Adipose-derived Stroma Cell Replicate 4 Mesenteric Adipose-derived Stroma Cells disease: Crohn's Disease; passage: 4; cell type: Fibroblast-like precursors isola... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2740125 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Crohn's Disease Adipose-derived Stroma Cell Replicate 5 Mesenteric Adipose-derived Stroma Cells disease: Crohn's Disease; passage: 4; cell type: Fibroblast-like precursors isola... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2740126 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Crohn's Disease Adipose-derived Stroma Cell Replicate 6 Mesenteric Adipose-derived Stroma Cells disease: Crohn's Disease; passage: 4; cell type: Fibroblast-like precursors isola... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease ulcerative colitis GSM2740133 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Ulcerative Colitis Adipose-derived Stroma Cell Replicate 1 Mesenteric Adipose-derived Stroma Cells disease: Ulcerative Colitis; passage: 4; cell type: Fibroblast-like precursors... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2740134 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Ulcerative Colitis Adipose-derived Stroma Cell Replicate 2 Mesenteric Adipose-derived Stroma Cells disease: Ulcerative Colitis; passage: 4; cell type: Fibroblast-like precursors... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2740135 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Ulcerative Colitis Adipose-derived Stroma Cell Replicate 3 Mesenteric Adipose-derived Stroma Cells disease: Ulcerative Colitis; passage: 4; cell type: Fibroblast-like precursors... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2740136 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Ulcerative Colitis Adipose-derived Stroma Cell Replicate 4 Mesenteric Adipose-derived Stroma Cells disease: Ulcerative Colitis; passage: 4; cell type: Fibroblast-like precursors... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2740137 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Ulcerative Colitis Adipose-derived Stroma Cell Replicate 5 Mesenteric Adipose-derived Stroma Cells disease: Ulcerative Colitis; passage: 4; cell type: Fibroblast-like precursors... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2740138 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Ulcerative Colitis Adipose-derived Stroma Cell Replicate 6 Mesenteric Adipose-derived Stroma Cells disease: Ulcerative Colitis; passage: 4; cell type: Fibroblast-like precursors... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

organism Homo sapiens GSE102524 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE102524 dataset_title: Inflammatory Bowel Disease-specific alterations in adipose-derived stroma cell transcriptional profiles organism: Homo sapiens assay_... keyword match keyword match: homo sapiens

Sample Group Preview

30 rows shown Show Hide

Study totals: Case 24 | Control 6 | Unassigned 0 | Excluded 0 | Ambiguous 0 30 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Cancer	Case	GSM2740115	Cancer Adipose-derived Stroma Cell Replicate 1	Mesenteric Adipose-derived Stroma Cells Disease: Cancer; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Explicit characteristic comparison arm detected.
Cancer	Case	GSM2740116	Cancer Adipose-derived Stroma Cell Replicate 2	Mesenteric Adipose-derived Stroma Cells Disease: Cancer; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Explicit characteristic comparison arm detected.
Cancer	Case	GSM2740117	Cancer Adipose-derived Stroma Cell Replicate 3	Mesenteric Adipose-derived Stroma Cells Disease: Cancer; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Explicit characteristic comparison arm detected.
Cancer	Case	GSM2740118	Cancer Adipose-derived Stroma Cell Replicate 4	Mesenteric Adipose-derived Stroma Cells Disease: Cancer; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Explicit characteristic comparison arm detected.
Cancer	Case	GSM2740119	Cancer Adipose-derived Stroma Cell Replicate 5	Mesenteric Adipose-derived Stroma Cells Disease: Cancer; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Explicit characteristic comparison arm detected.
Cancer	Case	GSM2740120	Cancer Adipose-derived Stroma Cell Replicate 6	Mesenteric Adipose-derived Stroma Cells Disease: Cancer; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Explicit characteristic comparison arm detected.
Crohn's disease	Case	GSM2740121	Crohn's Disease Adipose-derived Stroma Cell Replicate 1	Mesenteric Adipose-derived Stroma Cells Disease: Crohn's Disease; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Case marker detected.
Crohn's disease	Case	GSM2740122	Crohn's Disease Adipose-derived Stroma Cell Replicate 2	Mesenteric Adipose-derived Stroma Cells Disease: Crohn's Disease; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Case marker detected.
Crohn's disease	Case	GSM2740123	Crohn's Disease Adipose-derived Stroma Cell Replicate 3	Mesenteric Adipose-derived Stroma Cells Disease: Crohn's Disease; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Case marker detected.
Crohn's disease	Case	GSM2740124	Crohn's Disease Adipose-derived Stroma Cell Replicate 4	Mesenteric Adipose-derived Stroma Cells Disease: Crohn's Disease; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Case marker detected.
Crohn's disease	Case	GSM2740125	Crohn's Disease Adipose-derived Stroma Cell Replicate 5	Mesenteric Adipose-derived Stroma Cells Disease: Crohn's Disease; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Case marker detected.
Crohn's disease	Case	GSM2740126	Crohn's Disease Adipose-derived Stroma Cell Replicate 6	Mesenteric Adipose-derived Stroma Cells Disease: Crohn's Disease; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Case marker detected.
Obese	Case	GSM2740127	Obese Adipose-derived Stroma Cell Replicate 1	Mesenteric Adipose-derived Stroma Cells Disease: Obese; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Explicit characteristic comparison arm detected.
Obese	Case	GSM2740128	Obese Adipose-derived Stroma Cell Replicate 2	Mesenteric Adipose-derived Stroma Cells Disease: Obese; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Explicit characteristic comparison arm detected.
Obese	Case	GSM2740129	Obese Adipose-derived Stroma Cell Replicate 3	Mesenteric Adipose-derived Stroma Cells Disease: Obese; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Explicit characteristic comparison arm detected.
Obese	Case	GSM2740130	Obese Adipose-derived Stroma Cell Replicate 4	Mesenteric Adipose-derived Stroma Cells Disease: Obese; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Explicit characteristic comparison arm detected.
Obese	Case	GSM2740131	Obese Adipose-derived Stroma Cell Replicate 5	Mesenteric Adipose-derived Stroma Cells Disease: Obese; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Explicit characteristic comparison arm detected.
Obese	Case	GSM2740132	Obese Adipose-derived Stroma Cell Replicate 6	Mesenteric Adipose-derived Stroma Cells Disease: Obese; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Explicit characteristic comparison arm detected.
Ulcerative colitis	Case	GSM2740133	Ulcerative Colitis Adipose-derived Stroma Cell Replicate 1	Mesenteric Adipose-derived Stroma Cells Disease: Ulcerative Colitis; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Case marker detected.
Ulcerative colitis	Case	GSM2740134	Ulcerative Colitis Adipose-derived Stroma Cell Replicate 2	Mesenteric Adipose-derived Stroma Cells Disease: Ulcerative Colitis; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Case marker detected.
Ulcerative colitis	Case	GSM2740135	Ulcerative Colitis Adipose-derived Stroma Cell Replicate 3	Mesenteric Adipose-derived Stroma Cells Disease: Ulcerative Colitis; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Case marker detected.
Ulcerative colitis	Case	GSM2740136	Ulcerative Colitis Adipose-derived Stroma Cell Replicate 4	Mesenteric Adipose-derived Stroma Cells Disease: Ulcerative Colitis; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Case marker detected.
Ulcerative colitis	Case	GSM2740137	Ulcerative Colitis Adipose-derived Stroma Cell Replicate 5	Mesenteric Adipose-derived Stroma Cells Disease: Ulcerative Colitis; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Case marker detected.
Ulcerative colitis	Case	GSM2740138	Ulcerative Colitis Adipose-derived Stroma Cell Replicate 6	Mesenteric Adipose-derived Stroma Cells Disease: Ulcerative Colitis; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Case marker detected.
Control	Control	GSM2740109	Control Adipose-derived Stroma Cell Replicate 1	Mesenteric Adipose-derived Stroma Cells Disease: Control; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Sample-local control marker detected.
Control	Control	GSM2740110	Control Adipose-derived Stroma Cell Replicate 2	Mesenteric Adipose-derived Stroma Cells Disease: Control; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Sample-local control marker detected.
Control	Control	GSM2740111	Control Adipose-derived Stroma Cell Replicate 3	Mesenteric Adipose-derived Stroma Cells Disease: Control; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Sample-local control marker detected.
Control	Control	GSM2740112	Control Adipose-derived Stroma Cell Replicate 4	Mesenteric Adipose-derived Stroma Cells Disease: Control; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Sample-local control marker detected.
Control	Control	GSM2740113	Control Adipose-derived Stroma Cell Replicate 5	Mesenteric Adipose-derived Stroma Cells Disease: Control; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	Sample-local control marker detected.
Control	Control	GSM2740114	Control Adipose-derived Stroma Cell Replicate 6	Mesenteric Adipose-derived Stroma Cells Disease: Control; Passage: 4; Cell type: Fibroblast-like precursors isolated from whole mesenteric adipose tissue	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.