GSE90607

Fibrostenotic phenotype of fibroblasts in Crohn's disease is dependent on tissue stiffness and reversed by LOX inhibition

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

16 case / 8 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: 24 samples
Specimen: Tissue
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: de Bruyn JR, van den Brink GR, Steenkamer J, Buskens CJ, Bemelman WA, Meisner S, Muncan V, te Velde AA, D'Haens GR, Wildenberg ME
Contact name: Jessica Rebecca de Bruyn
Submission date: 2016-11-28
Last update: 2018-08-13
Organization: Academic Medical Center
Department: Gastroenterology and Hepatology
Public date: 2018-08-09
Experiment types: Expression profiling by array
Platforms: GPL10558 Illumina HumanHT-12 V4.0 expression beadchip
Series type: Series
SubSeries: Not available
BioProject: PRJNA355167

Summary

The results of this study indicate that stenotic fibroblasts exhibit an aberrant response to tissue stiffness with reduced MMP activity, leading to a perpetuous vicious circle of ever more fibrosis formation. Altering the microenvironment by LOX inhibition increases MMP activity and decreases ECM contraction, resulting in a potential anti-fibrotic agent for Crohn’s disease.

Overall design

Total RNA of human intestinal fibroblasts from 8 individual Crohn's disease patients. From every patient we used paired normal, inflamed and stenotic mucosa to isolate fibroblasts.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 24 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 Fibrostenotic Phenotype of Myofibroblasts in Crohn's Disease is Dependent on Tissue Stiffness and Reversed by LOX Inhibition. Journal of Crohn's & colitis, 2018 PubMed DOI	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, fibrosis Disease context came from Normalization rules.
Likely case group Crohn's disease 16 samples
Likely control group Healthy control 8 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, Fibrosis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 29672662.
Publication context: Fibrostenotic Phenotype of Myofibroblasts in Crohn's Disease is Dependent on Tissue Stiffness and Reversed by LOX Inhibition.. Journal of Crohn's & colitis, 2018. PMID 29672662. DOI 10.1093/ecco-jcc/jjy036.

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.
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

93 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source ileum GSM2407582 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407583 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407584 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407585 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407586 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407587 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407588 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407589 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407590 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407591 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407592 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407593 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407594 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407595 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407596 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407597 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407598 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407599 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407600 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407601 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407602 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407603 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407604 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM2407605 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: ileum sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE90607 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE90607 dataset_title: Fibrostenotic phenotype of fibroblasts in Crohn's disease is dependent on tissue stiffness and reversed by LOX inhibition organism: Ho... keyword match keyword match: microarray

disease Crohn's disease GSE90607 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease dataset_accession: GSE90607 dataset_title: Fibrostenotic phenotype of fibroblasts in Crohn's disease is dependent on tissue stiffness and reversed by LOX inhibition organism: Ho... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease fibrosis GSE90607 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis dataset_accession: GSE90607 dataset_title: Fibrostenotic phenotype of fibroblasts in Crohn's disease is dependent on tissue stiffness and reversed by LOX inhibition organism: Ho... controlled vocabulary controlled vocabulary disease match: fibrosis

disease Crohn's disease GSM2407582 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_stenotic_patientnumber46 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: stenotic; patient number: 46; gender: ... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407583 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_inflamed_patientnumber46 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 46; gender: ... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407584 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_normal_patientnumber17 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 17; gender: fema... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407585 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_inflamed_patientnumber17 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 17; gender: ... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407586 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_inflamed_patientnumber50 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 50; gender: ... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407587 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_normal_patientnumber13 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 13; gender: male... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407588 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_inflamed_patientnumber25 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 25; gender: ... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407589 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_normal_patientnumber46 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 46; gender: male... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407590 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_normal_patientnumber41 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 41; gender: fema... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407591 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_inflamed_patientnumber41 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 41; gender: ... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407592 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_stenotic_patientnumber41 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: stenotic; patient number: 41; gender: ... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407593 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_stenotic_patientnumber47 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: stenotic; patient number: 47; gender: ... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407594 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_stenotic_patientnumber25 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: stenotic; patient number: 25; gender: ... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407595 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_normal_patientnumber23 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 23; gender: fema... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407596 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_stenotic_patientnumber13 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: stenotic; patient number: 13; gender: ... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407597 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_stenotic_patientnumber23 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: stenotic; patient number: 23; gender: ... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407598 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_normal_patientnumber25 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 25; gender: fema... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407599 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_normal_patientnumber50 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 50; gender: male... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407600 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_inflamed_patientnumber13 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 13; gender: ... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407601 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_stenotic_patientnumber17 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: stenotic; patient number: 17; gender: ... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407602 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_inflamed_patientnumber47 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 47; gender: ... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407603 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_stenotic_patientnumber50 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: stenotic; patient number: 50; gender: ... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407604 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_normal_patientnumber47 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 47; gender: fema... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2407605 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease fibroblast_ileum_inflamed_patientnumber23 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 23; gender: ... controlled vocabulary controlled vocabulary disease match: Crohn's disease

organism Homo sapiens GSE90607 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE90607 dataset_title: Fibrostenotic phenotype of fibroblasts in Crohn's disease is dependent on tissue stiffness and reversed by LOX inhibition organism: Ho... keyword match keyword match: homo sapiens

sample_type inflamed tissue GSM2407583 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed fibroblast_ileum_inflamed_patientnumber46 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 46; gender: ... controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type normal tissue GSM2407584 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal fibroblast_ileum_normal_patientnumber17 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 17; gender: fema... controlled vocabulary controlled vocabulary sample type match: normal

sample_type inflamed tissue GSM2407585 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed fibroblast_ileum_inflamed_patientnumber17 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 17; gender: ... controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type inflamed tissue GSM2407586 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed fibroblast_ileum_inflamed_patientnumber50 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 50; gender: ... controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type normal tissue GSM2407587 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal fibroblast_ileum_normal_patientnumber13 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 13; gender: male... controlled vocabulary controlled vocabulary sample type match: normal

sample_type inflamed tissue GSM2407588 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed fibroblast_ileum_inflamed_patientnumber25 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 25; gender: ... controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type normal tissue GSM2407589 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal fibroblast_ileum_normal_patientnumber46 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 46; gender: male... controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM2407590 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal fibroblast_ileum_normal_patientnumber41 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 41; gender: fema... controlled vocabulary controlled vocabulary sample type match: normal

sample_type inflamed tissue GSM2407591 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed fibroblast_ileum_inflamed_patientnumber41 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 41; gender: ... controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type normal tissue GSM2407595 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal fibroblast_ileum_normal_patientnumber23 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 23; gender: fema... controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM2407598 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal fibroblast_ileum_normal_patientnumber25 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 25; gender: fema... controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM2407599 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal fibroblast_ileum_normal_patientnumber50 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 50; gender: male... controlled vocabulary controlled vocabulary sample type match: normal

sample_type inflamed tissue GSM2407600 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed fibroblast_ileum_inflamed_patientnumber13 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 13; gender: ... controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type inflamed tissue GSM2407602 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed fibroblast_ileum_inflamed_patientnumber47 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 47; gender: ... controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type normal tissue GSM2407604 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal fibroblast_ileum_normal_patientnumber47 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 47; gender: fema... controlled vocabulary controlled vocabulary sample type match: normal

sample_type inflamed tissue GSM2407605 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed fibroblast_ileum_inflamed_patientnumber23 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 23; gender: ... controlled vocabulary controlled vocabulary sample type match: inflamed

tissue intestine GSE90607 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal dataset_accession: GSE90607 dataset_title: Fibrostenotic phenotype of fibroblasts in Crohn's disease is dependent on tissue stiffness and reversed by LOX inhibition organism: Ho... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407582 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_stenotic_patientnumber46 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: stenotic; patient number: 46; gender: ... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407583 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_inflamed_patientnumber46 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 46; gender: ... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407584 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_normal_patientnumber17 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 17; gender: fema... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407585 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_inflamed_patientnumber17 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 17; gender: ... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407586 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_inflamed_patientnumber50 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 50; gender: ... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407587 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_normal_patientnumber13 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 13; gender: male... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407588 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_inflamed_patientnumber25 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 25; gender: ... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407589 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_normal_patientnumber46 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 46; gender: male... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407590 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_normal_patientnumber41 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 41; gender: fema... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407591 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_inflamed_patientnumber41 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 41; gender: ... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407592 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_stenotic_patientnumber41 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: stenotic; patient number: 41; gender: ... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407593 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_stenotic_patientnumber47 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: stenotic; patient number: 47; gender: ... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407594 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_stenotic_patientnumber25 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: stenotic; patient number: 25; gender: ... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407595 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_normal_patientnumber23 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 23; gender: fema... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407596 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_stenotic_patientnumber13 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: stenotic; patient number: 13; gender: ... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407597 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_stenotic_patientnumber23 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: stenotic; patient number: 23; gender: ... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407598 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_normal_patientnumber25 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 25; gender: fema... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407599 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_normal_patientnumber50 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 50; gender: male... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407600 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_inflamed_patientnumber13 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 13; gender: ... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407601 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_stenotic_patientnumber17 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: stenotic; patient number: 17; gender: ... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407602 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_inflamed_patientnumber47 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 47; gender: ... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407603 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_stenotic_patientnumber50 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: stenotic; patient number: 50; gender: ... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407604 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_normal_patientnumber47 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: normal; patient number: 47; gender: fema... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM2407605 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal fibroblast_ileum_inflamed_patientnumber23 intestinal fibroblast disease: Crohn's disease; tissue: ileum; cell type: fibroblast; phenotype: inflamed; patient number: 23; gender: ... controlled vocabulary controlled vocabulary tissue match: intestinal

Sample Group Preview

24 rows shown Show Hide

Study totals: Case 16 | Control 8 | Unassigned 0 | Excluded 0 | Ambiguous 0 24 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Crohn's disease	Case	GSM2407582	Fibroblast_ileum_stenotic_patientnumber46	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Stenotic; Patient number: 46; Gender: Male; Age at time of surgery (years): 31.1	Case marker detected.
Inflamed tissue	Case	GSM2407583	Fibroblast_ileum_inflamed_patientnumber46	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Inflamed; Patient number: 46; Gender: Male; Age at time of surgery (years): 31.1	Case marker detected.
Inflamed tissue	Case	GSM2407585	Fibroblast_ileum_inflamed_patientnumber17	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Inflamed; Patient number: 17; Gender: Female; Age at time of surgery (years): 52.5	Case marker detected.
Inflamed tissue	Case	GSM2407586	Fibroblast_ileum_inflamed_patientnumber50	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Inflamed; Patient number: 50; Gender: Male; Age at time of surgery (years): 22.7	Case marker detected.
Inflamed tissue	Case	GSM2407588	Fibroblast_ileum_inflamed_patientnumber25	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Inflamed; Patient number: 25; Gender: Female; Age at time of surgery (years): 22.7	Case marker detected.
Inflamed tissue	Case	GSM2407591	Fibroblast_ileum_inflamed_patientnumber41	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Inflamed; Patient number: 41; Gender: Female; Age at time of surgery (years): 26.4	Case marker detected.
Crohn's disease	Case	GSM2407592	Fibroblast_ileum_stenotic_patientnumber41	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Stenotic; Patient number: 41; Gender: Female; Age at time of surgery (years): 26.4	Case marker detected.
Crohn's disease	Case	GSM2407593	Fibroblast_ileum_stenotic_patientnumber47	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Stenotic; Patient number: 47; Gender: Female; Age at time of surgery (years): 31.7	Case marker detected.
Crohn's disease	Case	GSM2407594	Fibroblast_ileum_stenotic_patientnumber25	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Stenotic; Patient number: 25; Gender: Female; Age at time of surgery (years): 22.7	Case marker detected.
Crohn's disease	Case	GSM2407596	Fibroblast_ileum_stenotic_patientnumber13	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Stenotic; Patient number: 13; Gender: Male; Age at time of surgery (years): 26.6	Case marker detected.
Crohn's disease	Case	GSM2407597	Fibroblast_ileum_stenotic_patientnumber23	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Stenotic; Patient number: 23; Gender: Female; Age at time of surgery (years): 28.5	Case marker detected.
Inflamed tissue	Case	GSM2407600	Fibroblast_ileum_inflamed_patientnumber13	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Inflamed; Patient number: 13; Gender: Male; Age at time of surgery (years): 26.6	Case marker detected.
Crohn's disease	Case	GSM2407601	Fibroblast_ileum_stenotic_patientnumber17	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Stenotic; Patient number: 17; Gender: Female; Age at time of surgery (years): 52.5	Case marker detected.
Inflamed tissue	Case	GSM2407602	Fibroblast_ileum_inflamed_patientnumber47	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Inflamed; Patient number: 47; Gender: Female; Age at time of surgery (years): 31.7	Case marker detected.
Crohn's disease	Case	GSM2407603	Fibroblast_ileum_stenotic_patientnumber50	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Stenotic; Patient number: 50; Gender: Male; Age at time of surgery (years): 22.7	Case marker detected.
Inflamed tissue	Case	GSM2407605	Fibroblast_ileum_inflamed_patientnumber23	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Inflamed; Patient number: 23; Gender: Female; Age at time of surgery (years): 28.5	Case marker detected.
Healthy control	Control	GSM2407584	Fibroblast_ileum_normal_patientnumber17	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Normal; Patient number: 17; Gender: Female; Age at time of surgery (years): 52.5	Sample-local control marker detected.
Healthy control	Control	GSM2407587	Fibroblast_ileum_normal_patientnumber13	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Normal; Patient number: 13; Gender: Male; Age at time of surgery (years): 26.6	Sample-local control marker detected.
Healthy control	Control	GSM2407589	Fibroblast_ileum_normal_patientnumber46	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Normal; Patient number: 46; Gender: Male; Age at time of surgery (years): 31.1	Sample-local control marker detected.
Healthy control	Control	GSM2407590	Fibroblast_ileum_normal_patientnumber41	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Normal; Patient number: 41; Gender: Female; Age at time of surgery (years): 26.4	Sample-local control marker detected.
Healthy control	Control	GSM2407595	Fibroblast_ileum_normal_patientnumber23	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Normal; Patient number: 23; Gender: Female; Age at time of surgery (years): 28.5	Sample-local control marker detected.
Healthy control	Control	GSM2407598	Fibroblast_ileum_normal_patientnumber25	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Normal; Patient number: 25; Gender: Female; Age at time of surgery (years): 22.7	Sample-local control marker detected.
Healthy control	Control	GSM2407599	Fibroblast_ileum_normal_patientnumber50	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Normal; Patient number: 50; Gender: Male; Age at time of surgery (years): 22.7	Sample-local control marker detected.
Healthy control	Control	GSM2407604	Fibroblast_ileum_normal_patientnumber47	Intestinal fibroblast Disease: Crohn's disease; Tissue: Ileum; Cell type: Fibroblast; Phenotype: Normal; Patient number: 47; Gender: Female; Age at time of surgery (years): 31.7	Sample-local control marker detected.

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Carry Siftome's disease, organism, specimen, assay, data type, and accession into a validation project. Uncertain fields remain Unknown.

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Use as Discovery Cohort