GSE317503

Reference-guided genome assembly of long non-coding RNA transcripts reveals target genes associated with Crohn’s disease

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

0 case / 140 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.

Summary

RNA-seq of colon tissue from CD patients and non-IBD controls

Overall design

RNA-seq of colon tissue from CD patients and non-IBD controls *************************************************************** Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) for controlled access to the personally identifiable sequence data. ***************************************************************

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
140 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

  1. Reference-guided genome assembly of long non-coding rna transcripts reveals target genes associated with Crohn's disease. Scientific reports, 2026
Available

Metadata Quality Components

Analysis Readiness

Review before analysis
62% 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

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 complete case/control contrast is available.
  • Secondary RNA assay context should be analyzed separately from ordinary bulk RNA-seq.

Next Steps

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

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

  • Disease context Crohn's disease, inflammatory bowel disease Disease context came from Normalization rules.
  • Likely case group No case group detected 0 samples
  • Likely control group Non-inflamed tissue 140 samples

Intent Interpretation

  • Downgrade or exclusion reason Comparison: Unclear study design. Specimen: Tissue. 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: Crohn's disease, Inflammatory bowel disease.
  • Processed data is available for downstream review.
  • External evidence: PubMed links 1 publication; 1 DOI available: PMID 42185506.
  • Publication context: Reference-guided genome assembly of long non-coding rna transcripts reveals target genes associated with Crohn's disease.. Scientific reports, 2026. PMID 42185506. DOI 10.1038/s41598-026-54788-3.

Cautions

  • Comparison: Unclear study design. Specimen: Tissue. 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 - Tissue. 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 565 fields

Sample Group Preview

showing 50 of 140 preview rows
Show Hide
Study totals: Case 0 | Control 140 | Unassigned 0 | Excluded 0 | Ambiguous 0 showing 50 of 140 preview rows
Group Role Accession Title Source / characteristics Reason
Non-inflamed tissue Control GSM9473209 IBD_697394, colon Colon Tissue: Colon; Batch: F; Inflammation: Uninflamed; Disease status: NIBD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473210 IBD_413522, colon Colon Tissue: Colon; Batch: F; Inflammation: Uninflamed; Disease status: NIBD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473211 IBD_271984, colon Colon Tissue: Colon; Batch: H; Inflammation: Uninflamed; Disease status: CD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473212 IBD_154177, colon Colon Tissue: Colon; Batch: H; Inflammation: Uninflamed; Disease status: CD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473213 IBD_296868, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: CD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473214 IBD_974304, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: CD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473215 IBD_900592, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: CD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473216 IBD_571968, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: CD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473217 IBD_124014, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: CD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473218 IBD_621989, colon Colon Tissue: Colon; Batch: F; Inflammation: Uninflamed; Disease status: NIBD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473219 IBD_102541, colon Colon Tissue: Colon; Batch: F; Inflammation: Uninflamed; Disease status: NIBD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473220 IBD_699081, colon Colon Tissue: Colon; Batch: F; Inflammation: Uninflamed; Disease status: NIBD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473221 IBD_150644, colon Colon Tissue: Colon; Batch: F; Inflammation: Uninflamed; Disease status: CD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473222 IBD_664409, colon Colon Tissue: Colon; Batch: F; Inflammation: Uninflamed; Disease status: CD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473223 IBD_745873, colon Colon Tissue: Colon; Batch: F; Inflammation: Uninflamed; Disease status: NIBD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473224 IBD_565921, colon Colon Tissue: Colon; Batch: F; Inflammation: Uninflamed; Disease status: NIBD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473225 IBD_268860, colon Colon Tissue: Colon; Batch: F; Inflammation: Uninflamed; Disease status: CD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473226 IBD_888189, colon Colon Tissue: Colon; Batch: F; Inflammation: Uninflamed; Disease status: NIBD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473227 IBD_105888, colon Colon Tissue: Colon; Batch: F; Inflammation: Uninflamed; Disease status: CD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473228 IBD_462979, colon Colon Tissue: Colon; Batch: F; Inflammation: Uninflamed; Disease status: NIBD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473229 IBD_415959, colon Colon Tissue: Colon; Batch: F; Inflammation: Uninflamed; Disease status: NIBD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473230 IBD_614970, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: NIBD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473231 IBD_336603, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: CD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473232 IBD_328631, colon Colon Tissue: Colon; Batch: H; Inflammation: Uninflamed; Disease status: CD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473233 IBD_602009, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: CD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473234 IBD_961597, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: NIBD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473235 IBD_143391, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: NIBD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473236 IBD_849039, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: NIBD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473237 IBD_816534, colon Colon Tissue: Colon; Batch: H; Inflammation: Uninflamed; Disease status: CD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473238 IBD_654224, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: NIBD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473239 IBD_771279, colon Colon Tissue: Colon; Batch: H; Inflammation: Uninflamed; Disease status: CD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473240 IBD_467982, colon Colon Tissue: Colon; Batch: H; Inflammation: Uninflamed; Disease status: CD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473241 IBD_396332, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: CD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473242 IBD_794755, colon Colon Tissue: Colon; Batch: H; Inflammation: Uninflamed; Disease status: CD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473243 IBD_919154, colon Colon Tissue: Colon; Batch: H; Inflammation: Uninflamed; Disease status: CD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473244 IBD_555519, colon Colon Tissue: Colon; Batch: H; Inflammation: Uninflamed; Disease status: CD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473245 IBD_484581, colon Colon Tissue: Colon; Batch: H; Inflammation: Uninflamed; Disease status: CD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473246 IBD_839147, colon Colon Tissue: Colon; Batch: H; Inflammation: Uninflamed; Disease status: CD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473247 IBD_135118, colon Colon Tissue: Colon; Batch: H; Inflammation: Uninflamed; Disease status: CD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473248 IBD_954059, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: CD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473249 IBD_193721, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: CD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473250 IBD_560473, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: CD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473251 IBD_118727, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: CD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473252 IBD_301690, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: CD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473253 IBD_850257, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: CD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473254 IBD_268458, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: CD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473255 IBD_631005, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: CD; Sex: Female Control marker detected.
Non-inflamed tissue Control GSM9473256 IBD_346821, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: CD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473257 IBD_187482, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: CD; Sex: Male Control marker detected.
Non-inflamed tissue Control GSM9473258 IBD_845356, colon Colon Tissue: Colon; Batch: I; Inflammation: Uninflamed; Disease status: CD; Sex: Female Control marker detected.
90 additional control samples are hidden from this preview.

Use as Discovery Cohort

External Validation Finder

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