GSE173973

RNA-seq in untreated and Cadherin-11 Knockdown Human Intestinal Myofibroblast cells (HIMF)

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 / 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: bulk RNA-seq
Organism: Homo sapiens
Whole-study samples: 8 samples
Specimen: Tissue
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Li J, Zhao S
Contact name: Jiannan Li
Submission date: 2021-05-06
Last update: 2021-05-07
Organization: Cleveland Clinic
Department: Not available
Public date: 2021-05-07
Experiment types: Expression profiling by high throughput sequencing
Platforms: GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Series type: Series
SubSeries: Not available
BioProject: PRJNA727790

Summary

The goal of this experiment was to identify if there are any genes differentially expressed in Cadherin-11 KD HIMF

Overall design

RNA was isolated, cDNA libraries (100 bp, paired-end) were made at the University of Chicago Genomics Facility, and sequenced on an Illumina NovaSeq6000, in triplicates, according to standard protocols.

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	Publication context when PubMed identifiers are already known.	No match found

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: Treatment status metadata normalized where treatment is part of the comparison. 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 Disease context came from Normalization rules.
Likely case group Crohn's disease 4 samples
Likely control group Control 4 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.
Processed data is available for downstream review.

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.
Overall score capped because fewer than ten samples limit cohort confidence.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

No dataset warnings

Normalized Fields

39 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source colon GSM5283745 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Crohn's disease stricturedl colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM5283746 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Crohn's disease stricturedl colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM5283747 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Crohn's disease stricturedl colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM5283748 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Crohn's disease stricturedl colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM5283749 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Crohn's disease stricturedl colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM5283750 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Crohn's disease stricturedl colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM5283751 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Crohn's disease stricturedl colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM5283752 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Crohn's disease stricturedl colon sample-anatomical-source-v1 sample-local anatomical source

assay_type bulk RNA-seq GSE173973 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence bulk rna-seq dataset_accession: GSE173973 dataset_title: RNA-seq in untreated and Cadherin-11 Knockdown Human Intestinal Myofibroblast cells (HIMF) organism: Homo sapiens assay_type: bulk RN... keyword match keyword match: bulk rna-seq

disease Crohn's disease GSM5283745 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Untreated 48 hours replicate 1 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: scramble siRNA controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM5283746 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Untreated 48 hours replicate 2 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: scramble siRNA controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM5283747 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Untreated 48 hours replicate 3 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: scramble siRNA controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM5283748 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Untreated 48 hours replicate 4 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: scramble siRNA controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM5283749 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Cadherin-11 KD 48 hours replicate 1 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: Cadherin-11 siRNA controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM5283750 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Cadherin-11 KD 48 hours replicate 2 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: Cadherin-11 siRNA controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM5283751 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Cadherin-11 KD 48 hours replicate 3 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: Cadherin-11 siRNA controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM5283752 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Cadherin-11 KD 48 hours replicate 4 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: Cadherin-11 siRNA controlled vocabulary controlled vocabulary disease match: Crohn's disease

organism Homo sapiens GSE173973 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE173973 dataset_title: RNA-seq in untreated and Cadherin-11 Knockdown Human Intestinal Myofibroblast cells (HIMF) organism: Homo sapiens assay_type: bulk RN... keyword match keyword match: homo sapiens

tissue intestine GSE173973 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal dataset_accession: GSE173973 dataset_title: RNA-seq in untreated and Cadherin-11 Knockdown Human Intestinal Myofibroblast cells (HIMF) organism: Homo sapiens assay_type: bulk RN... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue colon GSM5283745 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Untreated 48 hours replicate 1 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: scramble siRNA controlled vocabulary controlled vocabulary tissue match: colon

tissue intestine GSM5283745 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Untreated 48 hours replicate 1 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: scramble siRNA controlled vocabulary controlled vocabulary tissue match: intestinal

tissue colon GSM5283746 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Untreated 48 hours replicate 2 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: scramble siRNA controlled vocabulary controlled vocabulary tissue match: colon

tissue intestine GSM5283746 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Untreated 48 hours replicate 2 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: scramble siRNA controlled vocabulary controlled vocabulary tissue match: intestinal

tissue colon GSM5283747 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Untreated 48 hours replicate 3 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: scramble siRNA controlled vocabulary controlled vocabulary tissue match: colon

tissue intestine GSM5283747 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Untreated 48 hours replicate 3 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: scramble siRNA controlled vocabulary controlled vocabulary tissue match: intestinal

tissue colon GSM5283748 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Untreated 48 hours replicate 4 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: scramble siRNA controlled vocabulary controlled vocabulary tissue match: colon

tissue intestine GSM5283748 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Untreated 48 hours replicate 4 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: scramble siRNA controlled vocabulary controlled vocabulary tissue match: intestinal

tissue colon GSM5283749 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Cadherin-11 KD 48 hours replicate 1 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: Cadherin-11 siRNA controlled vocabulary controlled vocabulary tissue match: colon

tissue intestine GSM5283749 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Cadherin-11 KD 48 hours replicate 1 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: Cadherin-11 siRNA controlled vocabulary controlled vocabulary tissue match: intestinal

tissue colon GSM5283750 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Cadherin-11 KD 48 hours replicate 2 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: Cadherin-11 siRNA controlled vocabulary controlled vocabulary tissue match: colon

tissue intestine GSM5283750 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Cadherin-11 KD 48 hours replicate 2 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: Cadherin-11 siRNA controlled vocabulary controlled vocabulary tissue match: intestinal

tissue colon GSM5283751 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Cadherin-11 KD 48 hours replicate 3 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: Cadherin-11 siRNA controlled vocabulary controlled vocabulary tissue match: colon

tissue intestine GSM5283751 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Cadherin-11 KD 48 hours replicate 3 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: Cadherin-11 siRNA controlled vocabulary controlled vocabulary tissue match: intestinal

tissue colon GSM5283752 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Cadherin-11 KD 48 hours replicate 4 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: Cadherin-11 siRNA controlled vocabulary controlled vocabulary tissue match: colon

tissue intestine GSM5283752 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Cadherin-11 KD 48 hours replicate 4 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: Cadherin-11 siRNA controlled vocabulary controlled vocabulary tissue match: intestinal

treatment_status untreated GSM5283745 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence untreated Untreated 48 hours replicate 1 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: scramble siRNA controlled vocabulary controlled vocabulary treatment status match: untreated

treatment_status untreated GSM5283746 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence untreated Untreated 48 hours replicate 2 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: scramble siRNA controlled vocabulary controlled vocabulary treatment status match: untreated

treatment_status untreated GSM5283747 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence untreated Untreated 48 hours replicate 3 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: scramble siRNA controlled vocabulary controlled vocabulary treatment status match: untreated

treatment_status untreated GSM5283748 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence untreated Untreated 48 hours replicate 4 Intestinal Myofibroblasts tissue: Crohn's disease stricturedl colon; passages: passage 8-10; treatment: scramble siRNA controlled vocabulary controlled vocabulary treatment status match: untreated

Sample Group Preview

8 rows shown Show Hide

Study totals: Case 4 | Control 4 | Unassigned 0 | Excluded 0 | Ambiguous 0 8 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Crohn's disease	Case	GSM5283749	Cadherin-11 KD 48 hours replicate 1	Intestinal Myofibroblasts Tissue: Crohn's disease stricturedl colon; Passages: Passage 8-10; Treatment: Cadherin-11 siRNA	Case marker detected.
Crohn's disease	Case	GSM5283750	Cadherin-11 KD 48 hours replicate 2	Intestinal Myofibroblasts Tissue: Crohn's disease stricturedl colon; Passages: Passage 8-10; Treatment: Cadherin-11 siRNA	Case marker detected.
Crohn's disease	Case	GSM5283751	Cadherin-11 KD 48 hours replicate 3	Intestinal Myofibroblasts Tissue: Crohn's disease stricturedl colon; Passages: Passage 8-10; Treatment: Cadherin-11 siRNA	Case marker detected.
Crohn's disease	Case	GSM5283752	Cadherin-11 KD 48 hours replicate 4	Intestinal Myofibroblasts Tissue: Crohn's disease stricturedl colon; Passages: Passage 8-10; Treatment: Cadherin-11 siRNA	Case marker detected.
Control	Control	GSM5283745	Untreated 48 hours replicate 1	Intestinal Myofibroblasts Tissue: Crohn's disease stricturedl colon; Passages: Passage 8-10; Treatment: Scramble siRNA	Control marker detected.
Control	Control	GSM5283746	Untreated 48 hours replicate 2	Intestinal Myofibroblasts Tissue: Crohn's disease stricturedl colon; Passages: Passage 8-10; Treatment: Scramble siRNA	Control marker detected.
Control	Control	GSM5283747	Untreated 48 hours replicate 3	Intestinal Myofibroblasts Tissue: Crohn's disease stricturedl colon; Passages: Passage 8-10; Treatment: Scramble siRNA	Control marker detected.
Control	Control	GSM5283748	Untreated 48 hours replicate 4	Intestinal Myofibroblasts Tissue: Crohn's disease stricturedl colon; Passages: Passage 8-10; Treatment: Scramble siRNA	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.