GSE46451

Effects of Inflammation and 5-ASA on ex vivo cultured ulcerative colitis biopsies

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

6 case / 6 control samples elsewhere in the study have incomplete or conflicting evidence; they are not included above

Patient pairs verified in indexed sample metadata: 0

A case/control comparison meeting these requirements is not confirmed.

Counts describe samples, not independent patients. Pair verification uses explicit subject identifiers in indexed sample metadata. Zero verified pairs does not establish that the study is unpaired; reported matched-normal design alone is insufficient.

Source: GEO
Assay: microarray
Organism: Homo sapiens
Whole-study samples: 12 samples
Specimen: Biopsy
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: MacFie TS, Boitsova T, Nijhuis A, Mein CA, Nuamah RA, Silver AR, Lindsay JO, Mein C
Contact name: Charles Mein
Submission date: 2013-04-29
Last update: 2018-08-13
Organization: Queen Mary University
Department: Genome Centre
Public date: 2013-12-12
Experiment types: Expression profiling by array
Platforms: GPL10558 Illumina HumanHT-12 V4.0 expression beadchip
Series type: Series
SubSeries: Not available
BioProject: PRJNA200560

Summary

To seek effects of inflammatory status and 5-aminosalicylic acid (5-ASA, mesalazine) exposure ex vivo on mRNA levels within rectal mucosal biopsies from patients with ulcerative colitis.

Overall design

A total of 12 biopsies were analysed, 3 biological replicates in each of 4 categories (inflamed with or without 5-ASA, non-inflamed with or without 5-ASA).

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 12 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

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 Ulcerative colitis Disease context came from Normalization rules.
Likely case group Inflamed tissue 6 samples
Likely control group Non-inflamed tissue 6 samples

Intent Interpretation

Downgrade or exclusion reason Downgraded assay: microarray cohorts are separated from the RNA-seq intent. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

Comparison: Disease/model vs control. Specimen: Biopsy. Comparison suitability: 0%.
Interpreted disease metadata: Ulcerative colitis.
Processed data is available for downstream review.

Cautions

Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
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.
Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.

Normalized Fields

100 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source colon GSM1130492 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1130492 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal mucosa tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1130493 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1130493 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal mucosa tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1130494 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1130494 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal mucosa tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1130495 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1130495 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal mucosa tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1130496 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1130496 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal mucosa tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1130497 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1130497 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal mucosa tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1130498 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1130498 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal mucosa tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1130499 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1130499 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal mucosa tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1130500 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1130500 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal mucosa tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1130501 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1130501 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal mucosa tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1130502 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1130502 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal mucosa tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1130503 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1130503 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rectal mucosa tissue: rectal mucosa biopsy cultured ex vivo sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE46451 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE46451 dataset_title: Effects of Inflammation and 5-ASA on ex vivo cultured ulcerative colitis biopsies organism: Homo sapiens assay_type: microarray proces... keyword match keyword match: microarray

collection_method biopsy GSM1130492 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy inflamed_no drug_rep1 rectal mucosa biopsy cultured ex vivo_inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes;... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1130493 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy inflamed_no drug_rep2 rectal mucosa biopsy cultured ex vivo_inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes;... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1130494 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy inflamed_no drug_rep3 rectal mucosa biopsy cultured ex vivo_inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes;... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1130495 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy inflamed_5-ASA_rep1 rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes; age... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1130496 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy inflamed_5-ASA_rep2 rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes; age... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1130497 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy inflamed_5-ASA_rep3 rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes; age... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1130498 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Non-inflamed_no drug_rep1 rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammati... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1130499 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Non-inflamed_no drug_rep2 rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammati... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1130500 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Non-inflamed_no drug_rep3 rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammati... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1130501 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Non-inflamed_5-ASA_rep1 rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: ... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1130502 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Non-inflamed_5-ASA_rep2 rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: ... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1130503 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Non-inflamed_5-ASA_rep3 rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: ... controlled vocabulary controlled vocabulary collection method match: biopsy

disease ulcerative colitis GSE46451 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis dataset_accession: GSE46451 dataset_title: Effects of Inflammation and 5-ASA on ex vivo cultured ulcerative colitis biopsies organism: Homo sapiens assay_type: microarray proces... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1130492 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis inflamed_no drug_rep1 rectal mucosa biopsy cultured ex vivo_inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes;... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1130493 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis inflamed_no drug_rep2 rectal mucosa biopsy cultured ex vivo_inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes;... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1130494 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis inflamed_no drug_rep3 rectal mucosa biopsy cultured ex vivo_inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes;... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1130495 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis inflamed_5-ASA_rep1 rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes; age... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1130496 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis inflamed_5-ASA_rep2 rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes; age... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1130497 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis inflamed_5-ASA_rep3 rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes; age... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1130498 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Non-inflamed_no drug_rep1 rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammati... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1130499 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Non-inflamed_no drug_rep2 rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammati... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1130500 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Non-inflamed_no drug_rep3 rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammati... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1130501 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Non-inflamed_5-ASA_rep1 rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: ... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1130502 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Non-inflamed_5-ASA_rep2 rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: ... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1130503 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Non-inflamed_5-ASA_rep3 rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: ... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

organism Homo sapiens GSE46451 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE46451 dataset_title: Effects of Inflammation and 5-ASA on ex vivo cultured ulcerative colitis biopsies organism: Homo sapiens assay_type: microarray proces... keyword match keyword match: homo sapiens

preparation_process culture GSM1130492 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence cultured inflamed_no drug_rep1 rectal mucosa biopsy cultured ex vivo_inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes;... controlled vocabulary controlled vocabulary preparation process match: cultured

preparation_process culture GSM1130493 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence cultured inflamed_no drug_rep2 rectal mucosa biopsy cultured ex vivo_inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes;... controlled vocabulary controlled vocabulary preparation process match: cultured

preparation_process culture GSM1130494 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence cultured inflamed_no drug_rep3 rectal mucosa biopsy cultured ex vivo_inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes;... controlled vocabulary controlled vocabulary preparation process match: cultured

preparation_process culture GSM1130495 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence cultured inflamed_5-ASA_rep1 rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes; age... controlled vocabulary controlled vocabulary preparation process match: cultured

preparation_process culture GSM1130496 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence cultured inflamed_5-ASA_rep2 rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes; age... controlled vocabulary controlled vocabulary preparation process match: cultured

preparation_process culture GSM1130497 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence cultured inflamed_5-ASA_rep3 rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes; age... controlled vocabulary controlled vocabulary preparation process match: cultured

preparation_process culture GSM1130498 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence cultured Non-inflamed_no drug_rep1 rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammati... controlled vocabulary controlled vocabulary preparation process match: cultured

preparation_process culture GSM1130499 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence cultured Non-inflamed_no drug_rep2 rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammati... controlled vocabulary controlled vocabulary preparation process match: cultured

preparation_process culture GSM1130500 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence cultured Non-inflamed_no drug_rep3 rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammati... controlled vocabulary controlled vocabulary preparation process match: cultured

preparation_process culture GSM1130501 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence cultured Non-inflamed_5-ASA_rep1 rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: ... controlled vocabulary controlled vocabulary preparation process match: cultured

preparation_process culture GSM1130502 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence cultured Non-inflamed_5-ASA_rep2 rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: ... controlled vocabulary controlled vocabulary preparation process match: cultured

preparation_process culture GSM1130503 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence cultured Non-inflamed_5-ASA_rep3 rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: ... controlled vocabulary controlled vocabulary preparation process match: cultured

primary_tissue primary tissue GSM1130492 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy inflamed_no drug_rep1 rectal mucosa biopsy cultured ex vivo_inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes;... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1130493 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy inflamed_no drug_rep2 rectal mucosa biopsy cultured ex vivo_inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes;... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1130494 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy inflamed_no drug_rep3 rectal mucosa biopsy cultured ex vivo_inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes;... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1130495 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy inflamed_5-ASA_rep1 rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes; age... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1130496 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy inflamed_5-ASA_rep2 rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes; age... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1130497 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy inflamed_5-ASA_rep3 rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes; age... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1130498 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Non-inflamed_no drug_rep1 rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammati... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1130499 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Non-inflamed_no drug_rep2 rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammati... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1130500 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Non-inflamed_no drug_rep3 rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammati... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1130501 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Non-inflamed_5-ASA_rep1 rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: ... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1130502 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Non-inflamed_5-ASA_rep2 rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: ... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1130503 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Non-inflamed_5-ASA_rep3 rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: ... controlled vocabulary controlled vocabulary primary tissue match: biopsy

sample_type inflamed tissue GSM1130492 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed inflamed_no drug_rep1 rectal mucosa biopsy cultured ex vivo_inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes;... controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type inflamed tissue GSM1130493 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed inflamed_no drug_rep2 rectal mucosa biopsy cultured ex vivo_inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes;... controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type inflamed tissue GSM1130494 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed inflamed_no drug_rep3 rectal mucosa biopsy cultured ex vivo_inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes;... controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type inflamed tissue GSM1130495 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed inflamed_5-ASA_rep1 rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes; age... controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type inflamed tissue GSM1130496 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed inflamed_5-ASA_rep2 rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes; age... controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type inflamed tissue GSM1130497 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed inflamed_5-ASA_rep3 rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes; age... controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type non-inflamed tissue GSM1130498 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence non-inflamed Non-inflamed_no drug_rep1 rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammati... controlled vocabulary controlled vocabulary sample type match: non-inflamed

sample_type non-inflamed tissue GSM1130499 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence non-inflamed Non-inflamed_no drug_rep2 rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammati... controlled vocabulary controlled vocabulary sample type match: non-inflamed

sample_type non-inflamed tissue GSM1130500 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence non-inflamed Non-inflamed_no drug_rep3 rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammati... controlled vocabulary controlled vocabulary sample type match: non-inflamed

sample_type non-inflamed tissue GSM1130501 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence non-inflamed Non-inflamed_5-ASA_rep1 rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: ... controlled vocabulary controlled vocabulary sample type match: non-inflamed

sample_type non-inflamed tissue GSM1130502 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence non-inflamed Non-inflamed_5-ASA_rep2 rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: ... controlled vocabulary controlled vocabulary sample type match: non-inflamed

sample_type non-inflamed tissue GSM1130503 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence non-inflamed Non-inflamed_5-ASA_rep3 rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: ... controlled vocabulary controlled vocabulary sample type match: non-inflamed

tissue colon GSE46451 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence rectal dataset_accession: GSE46451 dataset_title: Effects of Inflammation and 5-ASA on ex vivo cultured ulcerative colitis biopsies organism: Homo sapiens assay_type: microarray proces... controlled vocabulary controlled vocabulary tissue match: rectal

tissue colon GSM1130492 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence rectal inflamed_no drug_rep1 rectal mucosa biopsy cultured ex vivo_inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes;... controlled vocabulary controlled vocabulary tissue match: rectal

tissue colon GSM1130493 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence rectal inflamed_no drug_rep2 rectal mucosa biopsy cultured ex vivo_inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes;... controlled vocabulary controlled vocabulary tissue match: rectal

tissue colon GSM1130494 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence rectal inflamed_no drug_rep3 rectal mucosa biopsy cultured ex vivo_inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes;... controlled vocabulary controlled vocabulary tissue match: rectal

tissue colon GSM1130495 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence rectal inflamed_5-ASA_rep1 rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes; age... controlled vocabulary controlled vocabulary tissue match: rectal

tissue colon GSM1130496 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence rectal inflamed_5-ASA_rep2 rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes; age... controlled vocabulary controlled vocabulary tissue match: rectal

tissue colon GSM1130497 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence rectal inflamed_5-ASA_rep3 rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: yes; age... controlled vocabulary controlled vocabulary tissue match: rectal

tissue colon GSM1130498 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence rectal Non-inflamed_no drug_rep1 rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammati... controlled vocabulary controlled vocabulary tissue match: rectal

tissue colon GSM1130499 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence rectal Non-inflamed_no drug_rep2 rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammati... controlled vocabulary controlled vocabulary tissue match: rectal

tissue colon GSM1130500 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence rectal Non-inflamed_no drug_rep3 rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammati... controlled vocabulary controlled vocabulary tissue match: rectal

tissue colon GSM1130501 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence rectal Non-inflamed_5-ASA_rep1 rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: ... controlled vocabulary controlled vocabulary tissue match: rectal

tissue colon GSM1130502 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence rectal Non-inflamed_5-ASA_rep2 rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: ... controlled vocabulary controlled vocabulary tissue match: rectal

tissue colon GSM1130503 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence rectal Non-inflamed_5-ASA_rep3 rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA disease state: ulcerative colitis; tissue: rectal mucosa biopsy cultured ex vivo; inflammation: ... controlled vocabulary controlled vocabulary tissue match: rectal

Sample Group Preview

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Study totals: Case 6 | Control 6 | Unassigned 0 | Excluded 0 | Ambiguous 0 12 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Inflamed tissue	Case	GSM1130492	Inflamed_no drug_rep1	Rectal mucosa biopsy cultured ex vivo_inflamed_no drug Disease state: Ulcerative colitis; Tissue: Rectal mucosa biopsy cultured ex vivo; Inflammation: Yes; Agent: No drug	Case marker detected.
Inflamed tissue	Case	GSM1130493	Inflamed_no drug_rep2	Rectal mucosa biopsy cultured ex vivo_inflamed_no drug Disease state: Ulcerative colitis; Tissue: Rectal mucosa biopsy cultured ex vivo; Inflammation: Yes; Agent: No drug	Case marker detected.
Inflamed tissue	Case	GSM1130494	Inflamed_no drug_rep3	Rectal mucosa biopsy cultured ex vivo_inflamed_no drug Disease state: Ulcerative colitis; Tissue: Rectal mucosa biopsy cultured ex vivo; Inflammation: Yes; Agent: No drug	Case marker detected.
Inflamed tissue	Case	GSM1130495	Inflamed_5-ASA_rep1	Rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA Disease state: Ulcerative colitis; Tissue: Rectal mucosa biopsy cultured ex vivo; Inflammation: Yes; Agent: 5-ASA	Case marker detected.
Inflamed tissue	Case	GSM1130496	Inflamed_5-ASA_rep2	Rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA Disease state: Ulcerative colitis; Tissue: Rectal mucosa biopsy cultured ex vivo; Inflammation: Yes; Agent: 5-ASA	Case marker detected.
Inflamed tissue	Case	GSM1130497	Inflamed_5-ASA_rep3	Rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA Disease state: Ulcerative colitis; Tissue: Rectal mucosa biopsy cultured ex vivo; Inflammation: Yes; Agent: 5-ASA	Case marker detected.
Non-inflamed tissue	Control	GSM1130498	Non-inflamed_no drug_rep1	Rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug Disease state: Ulcerative colitis; Tissue: Rectal mucosa biopsy cultured ex vivo; Inflammation: No; Agent: No drug	Sample-local control marker detected.
Non-inflamed tissue	Control	GSM1130499	Non-inflamed_no drug_rep2	Rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug Disease state: Ulcerative colitis; Tissue: Rectal mucosa biopsy cultured ex vivo; Inflammation: No; Agent: No drug	Sample-local control marker detected.
Non-inflamed tissue	Control	GSM1130500	Non-inflamed_no drug_rep3	Rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug Disease state: Ulcerative colitis; Tissue: Rectal mucosa biopsy cultured ex vivo; Inflammation: No; Agent: No drug	Sample-local control marker detected.
Non-inflamed tissue	Control	GSM1130501	Non-inflamed_5-ASA_rep1	Rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA Disease state: Ulcerative colitis; Tissue: Rectal mucosa biopsy cultured ex vivo; Inflammation: No; Agent: 5-ASA	Sample-local control marker detected.
Non-inflamed tissue	Control	GSM1130502	Non-inflamed_5-ASA_rep2	Rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA Disease state: Ulcerative colitis; Tissue: Rectal mucosa biopsy cultured ex vivo; Inflammation: No; Agent: 5-ASA	Sample-local control marker detected.
Non-inflamed tissue	Control	GSM1130503	Non-inflamed_5-ASA_rep3	Rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA Disease state: Ulcerative colitis; Tissue: Rectal mucosa biopsy cultured ex vivo; Inflammation: No; Agent: 5-ASA	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.