GSE150961

Treatment Naïve and Follow-Up Pediatric Ulcerative Colitis Rectal Gene Expression

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

418 case / 0 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
418 samples
Specimen
Biopsy
Reported/interpreted study design
Unclear study design Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Mo A, Denson L, Hyams J, Gibson G
Contact name
Angela Mo
Submission date
2020-05-20
Last update
2021-05-20
Organization
Georgia Institute of Technology
Department
School of Biological Sciences
Public date
2021-05-20
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL21697 NextSeq 550 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA634153

Summary

PROTECT is a multicenter pediatric inception cohort study of response to standardized colitis therapy. In order to more explicitly model progression to colectomy within one year of diagnosis, we performed differential expression analysis between baseline rectal RNAseq biopsies of 21 patients who progressed to colectomy, and 310 who did not. We report rectal gene expression of pediatric patients with ulcerative colitis at diagnosis and at one year follow-up.

Overall design

418 rectal biopsies were obtained from pediatric ulcerative colitis patients during colonoscopy. Transcriptome profiling was performed with RNA-Seq.

Source Evidence

4 sources
Source Contribution Status
GEO

Original dataset metadata, sample metadata, source links, and GEO data availability flags.

Sample records
418 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

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: Treatment status metadata normalized where treatment is part of the comparison. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Analysis Readiness

Not ready
55% 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

15/15 pts

All samples are assigned to a case or control group.

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.
  • Critical dataset warnings must be resolved.

Next Steps

  • Resolve critical warnings before downstream analysis.

Analysis Preparation Checklist

4/6 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

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.

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

At least one comparison group has fewer than two samples.

Critical dataset warnings are present.

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

  • Disease context Ulcerative colitis Disease context came from Normalization rules.
  • Likely case group Ulcerative colitis 418 samples
  • Likely control group No control group detected 0 samples

Intent Interpretation

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

Ranking Facts

Supporting evidence

  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Interpreted disease metadata: Ulcerative colitis.
  • Processed data is available for downstream review.

Cautions

  • Comparison: Unclear study design. Specimen: Biopsy. Comparison suitability: 0%.
  • Downgraded for tissue search because study design or specimen source is unclear.
  • 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.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Missing or unclear metadata. Comparison - Unclear study design. Specimen - Biopsy. 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

Normalized Fields

showing 500 of 2425 fields

Sample Group Preview

showing 50 of 418 preview rows Show Hide
Study totals: Case 418 | Control 0 | Unassigned 0 | Excluded 0 | Ambiguous 0 showing 50 of 418 preview rows
Group Role Accession Title Source / characteristics Reason
Ulcerative colitis Case GSM4562625 Sample001 [Rectal biopsy] Rectal biopsy Individual: Ind314; Gender: M; Age at diagnosis: 5; Time of sampling: Baseline; Initial treatment: CS-IV; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562626 Sample002 [Rectal biopsy] Rectal biopsy Individual: Ind315; Gender: F; Age at diagnosis: 11; Time of sampling: Baseline; Initial treatment: 5ASA; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562627 Sample003 [Rectal biopsy] Rectal biopsy Individual: Ind001; Gender: M; Age at diagnosis: 14; Time of sampling: Baseline; Initial treatment: CS-Oral; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562628 Sample004 [Rectal biopsy] Rectal biopsy Individual: Ind002; Gender: F; Age at diagnosis: 16; Time of sampling: Baseline; Initial treatment: 5ASA; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562629 Sample005 [Rectal biopsy] Rectal biopsy Individual: Ind003; Gender: F; Age at diagnosis: 16; Time of sampling: Baseline; Initial treatment: CS-Oral; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562630 Sample006 [Rectal biopsy] Rectal biopsy Individual: Ind004; Gender: F; Age at diagnosis: 16; Time of sampling: Baseline; Initial treatment: 5ASA; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562631 Sample007 [Rectal biopsy] Rectal biopsy Individual: Ind005; Gender: F; Age at diagnosis: 12; Time of sampling: Baseline; Initial treatment: CS-Oral; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562632 Sample008 [Rectal biopsy] Rectal biopsy Individual: Ind006; Gender: M; Age at diagnosis: 11; Time of sampling: Baseline; Initial treatment: CS-IV; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562633 Sample009 [Rectal biopsy] Rectal biopsy Individual: Ind007; Gender: M; Age at diagnosis: 11; Time of sampling: Baseline; Initial treatment: CS-Oral; Colectomy: 1; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562634 Sample010 [Rectal biopsy] Rectal biopsy Individual: Ind008; Gender: F; Age at diagnosis: 15; Time of sampling: Baseline; Initial treatment: CS-IV; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562635 Sample011 [Rectal biopsy] Rectal biopsy Individual: Ind009; Gender: F; Age at diagnosis: 4; Time of sampling: Baseline; Initial treatment: CS-Oral; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562636 Sample012 [Rectal biopsy] Rectal biopsy Individual: Ind010; Gender: F; Age at diagnosis: 9; Time of sampling: Baseline; Initial treatment: CS-Oral; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562637 Sample013 [Rectal biopsy] Rectal biopsy Individual: Ind011; Gender: M; Age at diagnosis: 15; Time of sampling: Baseline; Initial treatment: CS-Oral; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562638 Sample014 [Rectal biopsy] Rectal biopsy Individual: Ind012; Gender: F; Age at diagnosis: 16; Time of sampling: Baseline; Initial treatment: CS-IV; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562639 Sample015 [Rectal biopsy] Rectal biopsy Individual: Ind013; Gender: F; Age at diagnosis: 12; Time of sampling: Baseline; Initial treatment: CS-IV; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562640 Sample016 [Rectal biopsy] Rectal biopsy Individual: Ind014; Gender: F; Age at diagnosis: 13; Time of sampling: Baseline; Initial treatment: 5ASA; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562641 Sample017 [Rectal biopsy] Rectal biopsy Individual: Ind015; Gender: F; Age at diagnosis: 14; Time of sampling: Baseline; Initial treatment: CS-IV; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562642 Sample018 [Rectal biopsy] Rectal biopsy Individual: Ind016; Gender: M; Age at diagnosis: 16; Time of sampling: Baseline; Initial treatment: 5ASA; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562643 Sample019 [Rectal biopsy] Rectal biopsy Individual: Ind017; Gender: F; Age at diagnosis: 16; Time of sampling: Baseline; Initial treatment: 5ASA; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562644 Sample020 [Rectal biopsy] Rectal biopsy Individual: Ind018; Gender: M; Age at diagnosis: 10; Time of sampling: Baseline; Initial treatment: CS-Oral; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562645 Sample021 [Rectal biopsy] Rectal biopsy Individual: Ind019; Gender: M; Age at diagnosis: 17; Time of sampling: Baseline; Initial treatment: CS-IV; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562646 Sample022 [Rectal biopsy] Rectal biopsy Individual: Ind298; Gender: F; Age at diagnosis: 13; Time of sampling: Baseline; Initial treatment: 5ASA; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562647 Sample023 [Rectal biopsy] Rectal biopsy Individual: Ind291; Gender: F; Age at diagnosis: 7; Time of sampling: Baseline; Initial treatment: CS-Oral; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562648 Sample024 [Rectal biopsy] Rectal biopsy Individual: Ind020; Gender: F; Age at diagnosis: 14; Time of sampling: Baseline; Initial treatment: CS-Oral; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562649 Sample025 [Rectal biopsy] Rectal biopsy Individual: Ind021; Gender: M; Age at diagnosis: 17; Time of sampling: Baseline; Initial treatment: 5ASA; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562650 Sample026 [Rectal biopsy] Rectal biopsy Individual: Ind022; Gender: F; Age at diagnosis: 15; Time of sampling: Baseline; Initial treatment: 5ASA; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562651 Sample027 [Rectal biopsy] Rectal biopsy Individual: Ind340; Gender: M; Age at diagnosis: 12; Time of sampling: Baseline; Initial treatment: CS-Oral; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562652 Sample028 [Rectal biopsy] Rectal biopsy Individual: Ind023; Gender: M; Age at diagnosis: 15; Time of sampling: Baseline; Initial treatment: 5ASA; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562653 Sample029 [Rectal biopsy] Rectal biopsy Individual: Ind283; Gender: F; Age at diagnosis: 7; Time of sampling: Baseline; Initial treatment: 5ASA; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562654 Sample030 [Rectal biopsy] Rectal biopsy Individual: Ind316; Gender: M; Age at diagnosis: 14; Time of sampling: Baseline; Initial treatment: CS-Oral; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562655 Sample031 [Rectal biopsy] Rectal biopsy Individual: Ind024; Gender: M; Age at diagnosis: 14; Time of sampling: Baseline; Initial treatment: CS-Oral; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562656 Sample032 [Rectal biopsy] Rectal biopsy Individual: Ind025; Gender: F; Age at diagnosis: 14; Time of sampling: Baseline; Initial treatment: CS-Oral; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562657 Sample033 [Rectal biopsy] Rectal biopsy Individual: Ind320; Gender: F; Age at diagnosis: 7; Time of sampling: Baseline; Initial treatment: CS-IV; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562658 Sample034 [Rectal biopsy] Rectal biopsy Individual: Ind317; Gender: F; Age at diagnosis: 9; Time of sampling: Baseline; Initial treatment: CS-Oral; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562659 Sample035 [Rectal biopsy] Rectal biopsy Individual: Ind026; Gender: M; Age at diagnosis: 15; Time of sampling: Baseline; Initial treatment: 5ASA; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562660 Sample036 [Rectal biopsy] Rectal biopsy Individual: Ind027; Gender: M; Age at diagnosis: 17; Time of sampling: Baseline; Initial treatment: CS-IV; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562661 Sample037 [Rectal biopsy] Rectal biopsy Individual: Ind028; Gender: M; Age at diagnosis: 14; Time of sampling: Baseline; Initial treatment: CS-Oral; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562662 Sample038 [Rectal biopsy] Rectal biopsy Individual: Ind029; Gender: M; Age at diagnosis: 16; Time of sampling: Baseline; Initial treatment: CS-IV; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562663 Sample039 [Rectal biopsy] Rectal biopsy Individual: Ind030; Gender: F; Age at diagnosis: 11; Time of sampling: Baseline; Initial treatment: 5ASA; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562664 Sample040 [Rectal biopsy] Rectal biopsy Individual: Ind284; Gender: M; Age at diagnosis: 11; Time of sampling: Baseline; Initial treatment: 5ASA; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562665 Sample041 [Rectal biopsy] Rectal biopsy Individual: Ind285; Gender: F; Age at diagnosis: 6; Time of sampling: Baseline; Initial treatment: 5ASA; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562666 Sample042 [Rectal biopsy] Rectal biopsy Individual: Ind031; Gender: M; Age at diagnosis: 17; Time of sampling: Baseline; Initial treatment: 5ASA; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562667 Sample043 [Rectal biopsy] Rectal biopsy Individual: Ind032; Gender: F; Age at diagnosis: 12; Time of sampling: Baseline; Initial treatment: 5ASA; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562668 Sample044 [Rectal biopsy] Rectal biopsy Individual: Ind033; Gender: M; Age at diagnosis: 14; Time of sampling: Baseline; Initial treatment: CS-IV; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562669 Sample045 [Rectal biopsy] Rectal biopsy Individual: Ind034; Gender: M; Age at diagnosis: 17; Time of sampling: Baseline; Initial treatment: CS-Oral; Colectomy: 1; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562670 Sample046 [Rectal biopsy] Rectal biopsy Individual: Ind035; Gender: F; Age at diagnosis: 8; Time of sampling: Baseline; Initial treatment: CS-IV; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562671 Sample047 [Rectal biopsy] Rectal biopsy Individual: Ind036; Gender: F; Age at diagnosis: 16; Time of sampling: Baseline; Initial treatment: CS-Oral; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562672 Sample048 [Rectal biopsy] Rectal biopsy Individual: Ind037; Gender: M; Age at diagnosis: 13; Time of sampling: Baseline; Initial treatment: 5ASA; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562673 Sample049 [Rectal biopsy] Rectal biopsy Individual: Ind038; Gender: M; Age at diagnosis: 16; Time of sampling: Baseline; Initial treatment: 5ASA; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM4562674 Sample050 [Rectal biopsy] Rectal biopsy Individual: Ind039; Gender: M; Age at diagnosis: 12; Time of sampling: Baseline; Initial treatment: CS-Oral; Colectomy: 0; Disease: Pediatric ulcerative colitis Case marker detected.
368 additional case samples are hidden from this preview.

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