GSE310282

RNAseq of colonic epithelial and lamina propria-derived Tregs

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

10 case / 1 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: 11 samples
Specimen: Tissue
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Lutter L, van Wijk F, Hoytema van Konijnenburg D
Contact name: Lisanne Lutter
Submission date: 2025-11-18
Last update: 2025-11-19
Organization: Amsterdam University Medical Center
Department: Not available
Public date: 2025-11-19
Experiment types: Expression profiling by high throughput sequencing
Platforms: GPL18573 Illumina NextSeq 500 (Homo sapiens)
Series type: Series
SubSeries: Not available
BioProject: PRJNA1365695

Summary

Local tissue adaptation by immune cells is of especially high importance in the small and large intestines, the largest mucosal barrier surface in the body. Recent work on tissue resident T cells has focused on CD8+ “tissue resident memory cells” or Trm. However, the human colon also contains different populations of CD4+ T cells, in mice referred to as “intraepithelial lymphocytes” and “lamina propria lymphocytes”. Our results uncover a pattern of compartmentalized tissue adaptation of human colonic CD4+ T cells in the steady state. This pattern is lost during active Inflammatory Bowel Disease, with potential detrimental effects on barrier maintenance and continued inflammation.

Overall design

RNA-seq profiling of sorted Tregs derived from the epithelium and lamina propria of colonic biopsies of patients with Crohn's disease and one control tissue from a patient with colorectal cancer.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 11 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: 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

Review before analysis

88% DE readiness

Contrast completeness

25/25 pts

Both case and control groups are present in the proposed grouping.

Minimum group size

8/20 pts

A contrast exists, but at least one group is below the minimum sample count.

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

At least one contrast group is below the minimum sample count.

Next Steps

Review blockers and update sample grouping or dataset selection before analysis.

Analysis Preparation Checklist

4/6 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

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

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.

Analysis readiness has blockers that must be resolved before DE.

Analysis preparation checklist contains blocked items.

At least one comparison group has fewer than two samples.

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, colorectal cancer, inflammatory bowel disease Disease context came from Normalization rules.
Likely case group Crohn's disease 10 samples
Likely control group Healthy control 1 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: Colorectal cancer, Crohn's disease, Inflammatory bowel 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.
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 GSM9293332 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM9293333 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM9293334 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM9293335 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM9293336 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM9293337 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM9293338 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM9293339 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM9293340 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM9293341 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM9293342 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

assay_type bulk RNA-seq GSE310282 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence bulk rna-seq dataset_accession: GSE310282 dataset_title: RNAseq of colonic epithelial and lamina propria-derived Tregs organism: Homo sapiens assay_type: bulk RNA-seq processed_data_availabl... keyword match keyword match: bulk rna-seq

disease Crohn's disease GSE310282 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease dataset_accession: GSE310282 dataset_title: RNAseq of colonic epithelial and lamina propria-derived Tregs organism: Homo sapiens assay_type: bulk RNA-seq processed_data_availabl... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease colorectal cancer GSE310282 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colorectal cancer dataset_accession: GSE310282 dataset_title: RNAseq of colonic epithelial and lamina propria-derived Tregs organism: Homo sapiens assay_type: bulk RNA-seq processed_data_availabl... controlled vocabulary controlled vocabulary disease match: colorectal cancer

disease inflammatory bowel disease GSE310282 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease dataset_accession: GSE310282 dataset_title: RNAseq of colonic epithelial and lamina propria-derived Tregs organism: Homo sapiens assay_type: bulk RNA-seq processed_data_availabl... controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease colorectal cancer GSM9293332 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colorectal cancer CD4CD25IEL colon tissue: colon; compartment: lamina propria; cell type: Treg (CD25high); sorted cell_number: 269; diagnosis: healthy colon of patient with colorectal cancer controlled vocabulary controlled vocabulary disease match: colorectal cancer

disease Crohn's disease GSM9293333 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD4CD25Hi012LPL colon tissue: colon; compartment: lamina propria; cell type: Treg (CD25high); sorted cell_number: 2500; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM9293334 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD4CD25hi011IEL colon tissue: colon; compartment: epithelium; cell type: Treg (CD25high); sorted cell_number: 10; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM9293335 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD4CD25hi011LPL colon tissue: colon; compartment: lamina propria; cell type: Treg (CD25high); sorted cell_number: 332; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM9293336 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD4CD25hi012IEL colon tissue: colon; compartment: epithelium; cell type: Treg (CD25high); sorted cell_number: 2500; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM9293337 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD4CD25hi013IEL colon tissue: colon; compartment: epithelium; cell type: Treg (CD25high); sorted cell_number: 117; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM9293338 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD4CD25hi013LPL colon tissue: colon; compartment: lamina propria; cell type: Treg (CD25high); sorted cell_number: 1548; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM9293339 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD4CD25hi014IEL colon tissue: colon; compartment: epithelium; cell type: Treg (CD25high); sorted cell_number: 495; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM9293340 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD4CD25hi014LPL colon tissue: colon; compartment: lamina propria; cell type: Treg (CD25high); sorted cell_number: 229; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM9293341 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD4CD25hi015IEL colon tissue: colon; compartment: epithelium; cell type: Treg (CD25high); sorted cell_number: 405; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM9293342 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD4CD25hi015LPL colon tissue: colon; compartment: lamina propria; cell type: Treg (CD25high); sorted cell_number: 396; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

organism Homo sapiens GSE310282 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE310282 dataset_title: RNAseq of colonic epithelial and lamina propria-derived Tregs organism: Homo sapiens assay_type: bulk RNA-seq processed_data_availabl... keyword match keyword match: homo sapiens

tissue colon GSE310282 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon dataset_accession: GSE310282 dataset_title: RNAseq of colonic epithelial and lamina propria-derived Tregs organism: Homo sapiens assay_type: bulk RNA-seq processed_data_availabl... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM9293332 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon CD4CD25IEL colon tissue: colon; compartment: lamina propria; cell type: Treg (CD25high); sorted cell_number: 269; diagnosis: healthy colon of patient with colorectal cancer controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM9293333 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon CD4CD25Hi012LPL colon tissue: colon; compartment: lamina propria; cell type: Treg (CD25high); sorted cell_number: 2500; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM9293334 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon CD4CD25hi011IEL colon tissue: colon; compartment: epithelium; cell type: Treg (CD25high); sorted cell_number: 10; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM9293335 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon CD4CD25hi011LPL colon tissue: colon; compartment: lamina propria; cell type: Treg (CD25high); sorted cell_number: 332; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM9293336 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon CD4CD25hi012IEL colon tissue: colon; compartment: epithelium; cell type: Treg (CD25high); sorted cell_number: 2500; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM9293337 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon CD4CD25hi013IEL colon tissue: colon; compartment: epithelium; cell type: Treg (CD25high); sorted cell_number: 117; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM9293338 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon CD4CD25hi013LPL colon tissue: colon; compartment: lamina propria; cell type: Treg (CD25high); sorted cell_number: 1548; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM9293339 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon CD4CD25hi014IEL colon tissue: colon; compartment: epithelium; cell type: Treg (CD25high); sorted cell_number: 495; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM9293340 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon CD4CD25hi014LPL colon tissue: colon; compartment: lamina propria; cell type: Treg (CD25high); sorted cell_number: 229; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM9293341 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon CD4CD25hi015IEL colon tissue: colon; compartment: epithelium; cell type: Treg (CD25high); sorted cell_number: 405; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM9293342 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon CD4CD25hi015LPL colon tissue: colon; compartment: lamina propria; cell type: Treg (CD25high); sorted cell_number: 396; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary tissue match: colon

Sample Group Preview

11 rows shown Show Hide

Study totals: Case 10 | Control 1 | Unassigned 0 | Excluded 0 | Ambiguous 0 11 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Crohn's disease	Case	GSM9293333	CD4CD25Hi012LPL	Colon Tissue: Colon; Compartment: Lamina propria; Cell type: Treg (CD25high); Sorted cell_number: 2500; Diagnosis: Crohn's disease	Case marker detected.
Crohn's disease	Case	GSM9293334	CD4CD25hi011IEL	Colon Tissue: Colon; Compartment: Epithelium; Cell type: Treg (CD25high); Sorted cell_number: 10; Diagnosis: Crohn's disease	Case marker detected.
Crohn's disease	Case	GSM9293335	CD4CD25hi011LPL	Colon Tissue: Colon; Compartment: Lamina propria; Cell type: Treg (CD25high); Sorted cell_number: 332; Diagnosis: Crohn's disease	Case marker detected.
Crohn's disease	Case	GSM9293336	CD4CD25hi012IEL	Colon Tissue: Colon; Compartment: Epithelium; Cell type: Treg (CD25high); Sorted cell_number: 2500; Diagnosis: Crohn's disease	Case marker detected.
Crohn's disease	Case	GSM9293337	CD4CD25hi013IEL	Colon Tissue: Colon; Compartment: Epithelium; Cell type: Treg (CD25high); Sorted cell_number: 117; Diagnosis: Crohn's disease	Case marker detected.
Crohn's disease	Case	GSM9293338	CD4CD25hi013LPL	Colon Tissue: Colon; Compartment: Lamina propria; Cell type: Treg (CD25high); Sorted cell_number: 1548; Diagnosis: Crohn's disease	Case marker detected.
Crohn's disease	Case	GSM9293339	CD4CD25hi014IEL	Colon Tissue: Colon; Compartment: Epithelium; Cell type: Treg (CD25high); Sorted cell_number: 495; Diagnosis: Crohn's disease	Case marker detected.
Crohn's disease	Case	GSM9293340	CD4CD25hi014LPL	Colon Tissue: Colon; Compartment: Lamina propria; Cell type: Treg (CD25high); Sorted cell_number: 229; Diagnosis: Crohn's disease	Case marker detected.
Crohn's disease	Case	GSM9293341	CD4CD25hi015IEL	Colon Tissue: Colon; Compartment: Epithelium; Cell type: Treg (CD25high); Sorted cell_number: 405; Diagnosis: Crohn's disease	Case marker detected.
Crohn's disease	Case	GSM9293342	CD4CD25hi015LPL	Colon Tissue: Colon; Compartment: Lamina propria; Cell type: Treg (CD25high); Sorted cell_number: 396; Diagnosis: Crohn's disease	Case marker detected.
Healthy control	Control	GSM9293332	CD4CD25IEL	Colon Tissue: Colon; Compartment: Lamina propria; Cell type: Treg (CD25high); Sorted cell_number: 269; Diagnosis: Healthy colon of patient with colorectal cancer	Sample-local control marker detected.

Use as Discovery Cohort

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