GSE33078

Comparison of intestinal surface CD3- refractory celiac disease type II (RCDII) cell lines with intestinal surface CD3+ cell lines of non-RCDII patients

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

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: 22 samples
Specimen: Cell line
Reported/interpreted study design: Unclear study design Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Schmitz F, Lai Y, Tjon J, Thompson A, Kooy-Winkelaar Y, Bergen J, Koning F
Contact name: Frederike Schmitz
Submission date: 2011-10-19
Last update: 2018-08-16
Organization: LUMC
Department: Immunohematology and Blood Transfusion
Public date: 2012-06-12
Experiment types: Expression profiling by array
Platforms: GPL6947 Illumina HumanHT-12 V3.0 expression beadchip
Series type: Series
SubSeries: Not available
BioProject: PRJNA149525

Summary

Analysis of transcriptional differences between aberrant (surface CD3-) RCDII cell lines and regular (surface CD3+) intraepithelial cell lines in order to characterize aberrant RCDII cells. All cell lines were cultured from duodenal biopsies of RCDII or non-RCDII (either celiac or non-celiac) patients.

Overall design

We compared 3 RCDII cell lines from RCDII patients P1-P3 with the following control cell lines: CD3+CD4+ T cell line from P1 and P3, CD3+CD8+ T cell line from P3 and mixed CD4/CD8+ T cell lines from non-RCDII patients. All control cells matched the phenotype of mature T cells (CD3+CD4+ and/or CD3+CD8+). Samples were randomly distributed among two BeadChips and measured in duplicates.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 22 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 Identification of a potential physiological precursor of aberrant cells in refractory coeliac disease type II. Gut, 2013 PubMed DOI	Available

Metadata Quality Components

Persisted metadata quality

93 pts

Clarity: 93%
Weight: 100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Only one side of the comparison is clearly grouped. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Anatomical source metadata normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Analysis Readiness

Not ready

43% DE readiness

Contrast completeness

10/25 pts

Only one side of the contrast is present; downstream DE needs both groups.

Minimum group size

0/20 pts

Minimum group size cannot be evaluated until a complete contrast exists.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

3/15 pts

Unassigned or review-needed samples remain before analysis.

Blocking warnings

0/10 pts

Critical warnings must be resolved before downstream analysis.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

No complete case/control contrast is available.
20 samples are still unassigned.
22 samples need manual grouping review.
Critical dataset warnings must be resolved.

Next Steps

Resolve unassigned or review-needed samples in the grouping table.
Resolve critical warnings before downstream analysis.

Analysis Preparation Checklist

3/6 ready

Group labels reviewed

Blocked

No complete case/control grouping exists yet.

Review the sample grouping table and assign both case and control groups.

Minimum sample count met

Blocked

At least one group has fewer than 2 samples.

Choose a larger dataset or merge only scientifically valid groups.

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

Verify that downloaded processed files contain usable count or expression identifiers.

Ambiguous samples handled

Needs review

22 review-needed samples and 20 unassigned samples remain.

Resolve ambiguous and unassigned samples before finalizing the contrast.

Exclusion decisions recorded

Ready

No hard-excluded samples were detected by the current rules.

Record any manual exclusions in the downstream analysis notes.

Source traceability preserved

Ready

The dataset and sample accessions can be traced back to GEO.

Keep GEO accessions with exported metadata.

Bioinformatician Review

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.

Analysis readiness has blockers that must be resolved before DE.

Analysis preparation checklist contains blocked items.

No complete case/control or treatment/control contrast is available.

At least one comparison group has fewer than two samples.

One or more samples are unassigned and need manual grouping decisions.

One or more samples were flagged for manual review.

Critical dataset warnings are present.

Assay context may require expert handling before DESeq2-style analysis.

Study design is model-system or unclear and should be reviewed before analysis.

Why This Is Ranked Here

Tumor vs normal

Not suitable Dataset does not meet the current suitability threshold.

Applied Review Decisions

No active review decisions affect this ranking.

Derived Classifications

Assay differs from search intent Microarray Search intent expects bulk RNA-seq. Assay came from Normalization rules.
Disease context Crohn's disease Disease context came from Normalization rules.
Likely case group Crohn's disease 2 samples
Likely control group No control group detected 0 samples

Intent Interpretation

Downgrade or exclusion reason Comparison: Unclear study design. Specimen: Cell line. Comparison suitability: 0%. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

Interpreted disease metadata: Crohn's disease.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 22760007.
Publication context: Identification of a potential physiological precursor of aberrant cells in refractory coeliac disease type II.. Gut, 2013. PMID 22760007. DOI 10.1136/gutjnl-2012-302265.

Cautions

Comparison: Unclear study design. Specimen: Cell line. Comparison suitability: 0%.
Downgraded for tissue search because it is a model-system experiment.
Downgraded for tissue search because study design or specimen source is unclear.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Excluded sample type flags reduce suitability.
Organoid or cell-line experiment downgraded for patient tissue search intent.
Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
Excluded model-system sample markers reduce suitability.
Overall score capped because comparison suitability is weak for the selected search intent.
Missing or unclear metadata. Comparison - Unclear study design. Specimen - Cell line. Comparison suitability: 0%.
Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

No clear control group was detected from normalized metadata.
Multiple sample type labels or exclusion flags were detected.
Cell line samples appear to be included.
Microarray expression context was detected; compare separately from RNA-seq cohorts.
Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Normalized Fields

54 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source colon GSM819201 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM819202 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE33078 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE33078 dataset_title: Comparison of intestinal surface CD3- refractory celiac disease type II (RCDII) cell lines with intestinal surface CD3+ cell lines of ... keyword match keyword match: microarray

disease Crohn's disease GSM819201 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease IEL5.1 intestinal cells disease status of patient: crohn's disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from crohns diseas... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM819202 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease IEL5.2 intestinal cells disease status of patient: crohn's disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from crohns diseas... controlled vocabulary controlled vocabulary disease match: Crohn's disease

excluded_sample_type cell line GSM819181 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line P3-CD4.1 intestinal cells disease status of patient: RCDII; surface marker expression: CD3+CD4+ CD8-; overall phenotype: T cell; patients: control clone from RCDII patient 3; ce... controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM819182 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line P3-CD4.2 intestinal cells disease status of patient: RCDII; surface marker expression: CD3+CD4+ CD8-; overall phenotype: T cell; patients: control clone from RCDII patient 3; ce... controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM819183 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line P1-CD4.1 intestinal cells disease status of patient: RCDII; surface marker expression: CD3+CD4+ CD8-; overall phenotype: T cell; patients: control line from RCDII patient 1; cel... controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM819184 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line P1-CD4.2 intestinal cells disease status of patient: RCDII; surface marker expression: CD3+CD4+ CD8-; overall phenotype: T cell; patients: control line from RCDII patient 1; cel... controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM819185 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line P1-CD8.1 intestinal cells disease status of patient: RCDII; surface marker expression: CD3+CD4- CD8+; overall phenotype: T cell; patients: control line from RCDII patient 1; cel... controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM819186 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line P1-CD8.2 intestinal cells disease status of patient: RCDII; surface marker expression: CD3+CD4- CD8+; overall phenotype: T cell; patients: control line from RCDII patient 1; cel... controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM819187 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line P1.1 intestinal cells disease status of patient: RCDII; surface marker expression: CD3-CD4-CD8-; overall phenotype: aberrant cell; patients: line RCDII patient 1; cell line/clon... controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM819188 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line P1.2 intestinal cells disease status of patient: RCDII; surface marker expression: CD3-CD4-CD8-; overall phenotype: aberrant cell; patients: line RCDII patient 1; cell line/clon... controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM819189 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line P2.1 intestinal cells disease status of patient: RCDII; surface marker expression: CD3-CD4-CD8-; overall phenotype: aberrant cell; patients: line RCDII patient 2; cell line/clon... controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM819190 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line P2.2 intestinal cells disease status of patient: RCDII; surface marker expression: CD3-CD4-CD8-; overall phenotype: aberrant cell; patients: line RCDII patient 2; cell line/clon... controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM819191 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line P3.1 intestinal cells disease status of patient: RCDII; surface marker expression: CD3-CD4-CD8-; overall phenotype: aberrant cell; patients: line RCDII patient 3; cell line/clon... controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM819192 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line P3.2 intestinal cells disease status of patient: RCDII; surface marker expression: CD3-CD4-CD8-; overall phenotype: aberrant cell; patients: line RCDII patient 3; cell line/clon... controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM819193 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line IEL1.1 intestinal cells disease status of patient: celiac disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from celiac disease... controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM819194 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line IEL1.2 intestinal cells disease status of patient: celiac disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from celiac disease... controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM819195 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line IEL2.1 intestinal cells disease status of patient: celiac disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from celiac disease... controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM819196 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line IEL2.2 intestinal cells disease status of patient: celiac disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from celiac disease... controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM819197 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line IEL3.1 intestinal cells disease status of patient: celiac disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from celiac disease... controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM819198 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line IEL3.2 intestinal cells disease status of patient: celiac disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from celiac disease... controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM819199 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line IEL4.1 intestinal cells disease status of patient: celiac disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from celiac disease... controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM819200 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line IEL4.2 intestinal cells disease status of patient: celiac disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from celiac disease... controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM819201 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line IEL5.1 intestinal cells disease status of patient: crohn's disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from crohns diseas... controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM819202 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line IEL5.2 intestinal cells disease status of patient: crohn's disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from crohns diseas... controlled vocabulary controlled vocabulary cell line match: cell line

organism Homo sapiens GSE33078 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE33078 dataset_title: Comparison of intestinal surface CD3- refractory celiac disease type II (RCDII) cell lines with intestinal surface CD3+ cell lines of ... keyword match keyword match: homo sapiens

tissue blood GSE33078 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood dataset_accession: GSE33078 dataset_title: Comparison of intestinal surface CD3- refractory celiac disease type II (RCDII) cell lines with intestinal surface CD3+ cell lines of ... controlled vocabulary controlled vocabulary tissue match: blood

tissue intestine GSE33078 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal dataset_accession: GSE33078 dataset_title: Comparison of intestinal surface CD3- refractory celiac disease type II (RCDII) cell lines with intestinal surface CD3+ cell lines of ... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM819181 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal P3-CD4.1 intestinal cells disease status of patient: RCDII; surface marker expression: CD3+CD4+ CD8-; overall phenotype: T cell; patients: control clone from RCDII patient 3; ce... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM819182 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal P3-CD4.2 intestinal cells disease status of patient: RCDII; surface marker expression: CD3+CD4+ CD8-; overall phenotype: T cell; patients: control clone from RCDII patient 3; ce... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM819183 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal P1-CD4.1 intestinal cells disease status of patient: RCDII; surface marker expression: CD3+CD4+ CD8-; overall phenotype: T cell; patients: control line from RCDII patient 1; cel... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM819184 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal P1-CD4.2 intestinal cells disease status of patient: RCDII; surface marker expression: CD3+CD4+ CD8-; overall phenotype: T cell; patients: control line from RCDII patient 1; cel... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM819185 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal P1-CD8.1 intestinal cells disease status of patient: RCDII; surface marker expression: CD3+CD4- CD8+; overall phenotype: T cell; patients: control line from RCDII patient 1; cel... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM819186 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal P1-CD8.2 intestinal cells disease status of patient: RCDII; surface marker expression: CD3+CD4- CD8+; overall phenotype: T cell; patients: control line from RCDII patient 1; cel... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM819187 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal P1.1 intestinal cells disease status of patient: RCDII; surface marker expression: CD3-CD4-CD8-; overall phenotype: aberrant cell; patients: line RCDII patient 1; cell line/clon... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM819188 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal P1.2 intestinal cells disease status of patient: RCDII; surface marker expression: CD3-CD4-CD8-; overall phenotype: aberrant cell; patients: line RCDII patient 1; cell line/clon... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM819189 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal P2.1 intestinal cells disease status of patient: RCDII; surface marker expression: CD3-CD4-CD8-; overall phenotype: aberrant cell; patients: line RCDII patient 2; cell line/clon... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM819190 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal P2.2 intestinal cells disease status of patient: RCDII; surface marker expression: CD3-CD4-CD8-; overall phenotype: aberrant cell; patients: line RCDII patient 2; cell line/clon... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM819191 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal P3.1 intestinal cells disease status of patient: RCDII; surface marker expression: CD3-CD4-CD8-; overall phenotype: aberrant cell; patients: line RCDII patient 3; cell line/clon... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM819192 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal P3.2 intestinal cells disease status of patient: RCDII; surface marker expression: CD3-CD4-CD8-; overall phenotype: aberrant cell; patients: line RCDII patient 3; cell line/clon... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM819193 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal IEL1.1 intestinal cells disease status of patient: celiac disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from celiac disease... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM819194 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal IEL1.2 intestinal cells disease status of patient: celiac disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from celiac disease... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM819195 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal IEL2.1 intestinal cells disease status of patient: celiac disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from celiac disease... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM819196 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal IEL2.2 intestinal cells disease status of patient: celiac disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from celiac disease... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM819197 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal IEL3.1 intestinal cells disease status of patient: celiac disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from celiac disease... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM819198 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal IEL3.2 intestinal cells disease status of patient: celiac disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from celiac disease... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM819199 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal IEL4.1 intestinal cells disease status of patient: celiac disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from celiac disease... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM819200 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal IEL4.2 intestinal cells disease status of patient: celiac disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from celiac disease... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue colon GSM819201 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon IEL5.1 intestinal cells disease status of patient: crohn's disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from crohns diseas... controlled vocabulary controlled vocabulary tissue match: colon

tissue intestine GSM819201 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal IEL5.1 intestinal cells disease status of patient: crohn's disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from crohns diseas... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue colon GSM819202 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon IEL5.2 intestinal cells disease status of patient: crohn's disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from crohns diseas... controlled vocabulary controlled vocabulary tissue match: colon

tissue intestine GSM819202 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal IEL5.2 intestinal cells disease status of patient: crohn's disease; surface marker expression: CD3+CD4+CD8+; overall phenotype: T cell; patients: control line from crohns diseas... controlled vocabulary controlled vocabulary tissue match: intestinal

Sample Group Preview

22 rows shown Show Hide

Study totals: Case 2 | Control 0 | Unassigned 20 | Excluded 0 | Ambiguous 0 22 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Crohn's disease	Case	GSM819201	IEL5.1	Intestinal cells Disease status of patient: Crohn's disease; Surface marker expression: CD3+CD4+CD8+; Overall phenotype: T cell; Patients: Control line from crohns disease patient; Cell line/clone: Line; Tissue: Colon; Gender: F	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Crohn's disease	Case	GSM819202	IEL5.2	Intestinal cells Disease status of patient: Crohn's disease; Surface marker expression: CD3+CD4+CD8+; Overall phenotype: T cell; Patients: Control line from crohns disease patient; Cell line/clone: Line; Tissue: Colon; Gender: F	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Unassigned	Unassigned	GSM819181	P3-CD4.1	Intestinal cells Disease status of patient: RCDII; Surface marker expression: CD3+CD4+ CD8-; Overall phenotype: T cell; Patients: Control clone from RCDII patient 3; Cell line/clone: Clone; Tissue: Duodenum; Gender: M	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Unassigned	Unassigned	GSM819182	P3-CD4.2	Intestinal cells Disease status of patient: RCDII; Surface marker expression: CD3+CD4+ CD8-; Overall phenotype: T cell; Patients: Control clone from RCDII patient 3; Cell line/clone: Clone; Tissue: Duodenum; Gender: M	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Unassigned	Unassigned	GSM819183	P1-CD4.1	Intestinal cells Disease status of patient: RCDII; Surface marker expression: CD3+CD4+ CD8-; Overall phenotype: T cell; Patients: Control line from RCDII patient 1; Cell line/clone: Line; Tissue: Duodenum; Gender: F	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Unassigned	Unassigned	GSM819184	P1-CD4.2	Intestinal cells Disease status of patient: RCDII; Surface marker expression: CD3+CD4+ CD8-; Overall phenotype: T cell; Patients: Control line from RCDII patient 1; Cell line/clone: Line; Tissue: Duodenum; Gender: F	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Unassigned	Unassigned	GSM819185	P1-CD8.1	Intestinal cells Disease status of patient: RCDII; Surface marker expression: CD3+CD4- CD8+; Overall phenotype: T cell; Patients: Control line from RCDII patient 1; Cell line/clone: Line; Tissue: Duodenum; Gender: F	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Unassigned	Unassigned	GSM819186	P1-CD8.2	Intestinal cells Disease status of patient: RCDII; Surface marker expression: CD3+CD4- CD8+; Overall phenotype: T cell; Patients: Control line from RCDII patient 1; Cell line/clone: Line; Tissue: Duodenum; Gender: F	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Unassigned	Unassigned	GSM819187	P1.1	Intestinal cells Disease status of patient: RCDII; Surface marker expression: CD3-CD4-CD8-; Overall phenotype: Aberrant cell; Patients: Line RCDII patient 1; Cell line/clone: Line; Tissue: Duodenum; Gender: F	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Unassigned	Unassigned	GSM819188	P1.2	Intestinal cells Disease status of patient: RCDII; Surface marker expression: CD3-CD4-CD8-; Overall phenotype: Aberrant cell; Patients: Line RCDII patient 1; Cell line/clone: Line; Tissue: Duodenum; Gender: F	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Unassigned	Unassigned	GSM819189	P2.1	Intestinal cells Disease status of patient: RCDII; Surface marker expression: CD3-CD4-CD8-; Overall phenotype: Aberrant cell; Patients: Line RCDII patient 2; Cell line/clone: Line; Tissue: Duodenum; Gender: M	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Unassigned	Unassigned	GSM819190	P2.2	Intestinal cells Disease status of patient: RCDII; Surface marker expression: CD3-CD4-CD8-; Overall phenotype: Aberrant cell; Patients: Line RCDII patient 2; Cell line/clone: Line; Tissue: Duodenum; Gender: M	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Unassigned	Unassigned	GSM819191	P3.1	Intestinal cells Disease status of patient: RCDII; Surface marker expression: CD3-CD4-CD8-; Overall phenotype: Aberrant cell; Patients: Line RCDII patient 3; Cell line/clone: Line; Tissue: Duodenum; Gender: M	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Unassigned	Unassigned	GSM819192	P3.2	Intestinal cells Disease status of patient: RCDII; Surface marker expression: CD3-CD4-CD8-; Overall phenotype: Aberrant cell; Patients: Line RCDII patient 3; Cell line/clone: Line; Tissue: Duodenum; Gender: M	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Unassigned	Unassigned	GSM819193	IEL1.1	Intestinal cells Disease status of patient: Celiac disease; Surface marker expression: CD3+CD4+CD8+; Overall phenotype: T cell; Patients: Control line from celiac disease patient; Cell line/clone: Line; Tissue: Duodenum; Gender: M	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Unassigned	Unassigned	GSM819194	IEL1.2	Intestinal cells Disease status of patient: Celiac disease; Surface marker expression: CD3+CD4+CD8+; Overall phenotype: T cell; Patients: Control line from celiac disease patient; Cell line/clone: Line; Tissue: Duodenum; Gender: M	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Unassigned	Unassigned	GSM819195	IEL2.1	Intestinal cells Disease status of patient: Celiac disease; Surface marker expression: CD3+CD4+CD8+; Overall phenotype: T cell; Patients: Control line from celiac disease patient; Cell line/clone: Line; Tissue: Duodenum; Gender: M	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Unassigned	Unassigned	GSM819196	IEL2.2	Intestinal cells Disease status of patient: Celiac disease; Surface marker expression: CD3+CD4+CD8+; Overall phenotype: T cell; Patients: Control line from celiac disease patient; Cell line/clone: Line; Tissue: Duodenum; Gender: M	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Unassigned	Unassigned	GSM819197	IEL3.1	Intestinal cells Disease status of patient: Celiac disease; Surface marker expression: CD3+CD4+CD8+; Overall phenotype: T cell; Patients: Control line from celiac disease patient; Cell line/clone: Line; Tissue: Duodenum; Gender: F	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Unassigned	Unassigned	GSM819198	IEL3.2	Intestinal cells Disease status of patient: Celiac disease; Surface marker expression: CD3+CD4+CD8+; Overall phenotype: T cell; Patients: Control line from celiac disease patient; Cell line/clone: Line; Tissue: Duodenum; Gender: F	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Unassigned	Unassigned	GSM819199	IEL4.1	Intestinal cells Disease status of patient: Celiac disease; Surface marker expression: CD3+CD4+CD8+; Overall phenotype: T cell; Patients: Control line from celiac disease patient; Cell line/clone: Line; Tissue: Duodenum; Gender: F	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Unassigned	Unassigned	GSM819200	IEL4.2	Intestinal cells Disease status of patient: Celiac disease; Surface marker expression: CD3+CD4+CD8+; Overall phenotype: T cell; Patients: Control line from celiac disease patient; Cell line/clone: Line; Tissue: Duodenum; Gender: F	cell line: Standalone model-system marker retained for comparison grouping: cell line.

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.

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Use as Discovery Cohort