GSE169569

Small RNA-seq data of peripheral blood obtained from treatment-näive IBD patients and control individuals (small RNA-Seq I)

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

110 case / 95 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

Comperhensive analysis of blood transcriptomes obtained from treatment-näive IBD patients.

Overall design

Total RNA extracted from peripheral blood samples (n = 205) was used to generate small RNA libraries employing TruSeq Small RNA Sample Preparation Kit (Illumina) according to the manufacturer’s instructions.

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
205 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. Detailed Transcriptional Landscape of Peripheral Blood Points to Increased Neutrophil Activation in Treatment-Naïve Inflammatory Bowel Disease. Journal of Crohn's & colitis, 2022
Available

Metadata Quality Components

Analysis Readiness

Review before analysis
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

  • 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

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.

Analysis readiness has blockers that must be resolved 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

  • Disease context Crohn's disease, inflammatory bowel disease, ulcerative colitis Disease context came from Normalization rules.
  • Likely case group Ulcerative colitis 110 samples
  • Likely control group Mixed controls 95 samples

Intent Interpretation

  • Downgrade or exclusion reason Downgraded for tissue search because it is a biofluid cohort. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

  • Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis.
  • Processed data is available for downstream review.
  • External evidence: PubMed links 1 publication; 1 DOI available: PMID 35022690.
  • Publication context: Detailed Transcriptional Landscape of Peripheral Blood Points to Increased Neutrophil Activation in Treatment-Naïve Inflammatory Bowel Disease.. Journal of Crohn's & colitis, 2022. PMID 35022690. DOI 10.1093/ecco-jcc/jjac003.

Cautions

  • Downgraded for tissue search because it is a biofluid cohort.
  • Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
  • Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
  • Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Normalized Fields

showing 500 of 614 fields

Sample Group Preview

showing 100 of 205 preview rows
Show Hide
Study totals: Case 110 | Control 95 | Unassigned 0 | Excluded 0 | Ambiguous 0 showing 100 of 205 preview rows
Group Role Accession Title Source / characteristics Reason
Ulcerative colitis Case GSM5209636 D5595 Peripheral blood Sex: Male; Age: 39; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209638 D5598 Peripheral blood Sex: Female; Age: 31; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209639 D5599 Peripheral blood Sex: Male; Age: 22; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209642 D5602 Peripheral blood Sex: Female; Age: 30; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209647 D5607 Peripheral blood Sex: Female; Age: 27; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209650 D5610 Peripheral blood Sex: Male; Age: 57; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209652 D5613 Peripheral blood Sex: Female; Age: 20; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209654 D5616 Peripheral blood Sex: Male; Age: 27; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209655 D5617 Peripheral blood Sex: Male; Age: 32; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209657 D5499 Peripheral blood Sex: Female; Age: 35; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209659 D5501 Peripheral blood Sex: Male; Age: 21; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209660 D5502 Peripheral blood Sex: Male; Age: 62; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209661 D5503 Peripheral blood Sex: Female; Age: 41; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209662 D5505 Peripheral blood Sex: Female; Age: 22; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209663 D5506 Peripheral blood Sex: Female; Age: 18; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209664 D5508 Peripheral blood Sex: Male; Age: 20; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209665 D5509 Peripheral blood Sex: Female; Age: 29; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209666 D5510 Peripheral blood Sex: Male; Age: 46; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209669 D5514 Peripheral blood Sex: Male; Age: 32; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209671 D5519 Peripheral blood Sex: Male; Age: 76; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209672 D5521 Peripheral blood Sex: Female; Age: 23; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209678 D5527 Peripheral blood Sex: Male; Age: 26; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209679 D5528 Peripheral blood Sex: Male; Age: 19; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209680 D5529 Peripheral blood Sex: Female; Age: 60; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209681 D5530 Peripheral blood Sex: Female; Age: 17; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209682 D5531 Peripheral blood Sex: Female; Age: 41; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209683 D5537 Peripheral blood Sex: Female; Age: 48; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209684 D5538 Peripheral blood Sex: Female; Age: 26; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209685 D5542 Peripheral blood Sex: Male; Age: 35; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209686 D5543 Peripheral blood Sex: Female; Age: 22; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209687 D5544 Peripheral blood Sex: Female; Age: 73; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209688 D5545 Peripheral blood Sex: Male; Age: 69; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209710 E04811 Peripheral blood Sex: Male; Age: 21; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209711 E04812 Peripheral blood Sex: Male; Age: 34; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209713 D5451 Peripheral blood Sex: Female; Age: 31; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209714 D5452 Peripheral blood Sex: Female; Age: 40; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209715 D5454 Peripheral blood Sex: Female; Age: 24; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209716 D5455 Peripheral blood Sex: Male; Age: 24; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209719 D5458 Peripheral blood Sex: Female; Age: 25; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209722 D5462 Peripheral blood Sex: Male; Age: 32; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209723 D5463 Peripheral blood Sex: Female; Age: 23; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209724 D5464 Peripheral blood Sex: Male; Age: 36; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209725 D5465 Peripheral blood Sex: Male; Age: 26; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209726 D5466 Peripheral blood Sex: Female; Age: 23; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209727 D5467 Peripheral blood Sex: Male; Age: 36; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209728 D5470 Peripheral blood Sex: Female; Age: 40; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209729 D5472 Peripheral blood Sex: Female; Age: 26; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209730 D5473 Peripheral blood Sex: Female; Age: 18; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209732 D5475 Peripheral blood Sex: Female; Age: 24; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209733 D5476 Peripheral blood Sex: Male; Age: 32; Diagnosis: Ulcerative colitis Case marker detected.
60 additional case samples are hidden from this preview.
Control Control GSM5209635 D5594 Peripheral blood Sex: Female; Age: 20; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209637 D5597 Peripheral blood Sex: Female; Age: 56; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209640 D5600 Peripheral blood Sex: Male; Age: 32; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209641 D5601 Peripheral blood Sex: Female; Age: 32; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209643 D5603 Peripheral blood Sex: Male; Age: 30; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209644 D5604 Peripheral blood Sex: Female; Age: 18; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209645 D5605 Peripheral blood Sex: Female; Age: 60; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209646 D5606 Peripheral blood Sex: Male; Age: 33; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209648 D5608 Peripheral blood Sex: Male; Age: 30; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209649 D5609 Peripheral blood Sex: Female; Age: 34; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209651 D5611 Peripheral blood Sex: Male; Age: 27; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209653 D5614 Peripheral blood Sex: Female; Age: 30; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209656 D5498 Peripheral blood Sex: Female; Age: 72; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209658 D5500 Peripheral blood Sex: Female; Age: 24; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209667 D5511 Peripheral blood Sex: Male; Age: 31; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209668 D5513 Peripheral blood Sex: Female; Age: 34; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209670 D5518 Peripheral blood Sex: Female; Age: 49; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209673 D5522 Peripheral blood Sex: Male; Age: 37; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209674 D5523 Peripheral blood Sex: Male; Age: 30; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209675 D5524 Peripheral blood Sex: Male; Age: 64; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209676 D5525 Peripheral blood Sex: Male; Age: 23; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209677 D5526 Peripheral blood Sex: Female; Age: 24; Diagnosis: Symptomatic control Sample-local control marker detected.
Healthy control Control GSM5209689 D5654 Peripheral blood Sex: Male; Age: 57; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5209690 D5655 Peripheral blood Sex: Female; Age: 50; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5209691 D5656 Peripheral blood Sex: Male; Age: 27; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5209692 D5657 Peripheral blood Sex: Male; Age: 69; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5209693 D5658 Peripheral blood Sex: Male; Age: 28; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5209694 D5659 Peripheral blood Sex: Female; Age: 51; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5209695 D5660 Peripheral blood Sex: Male; Age: 64; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5209696 D5661 Peripheral blood Sex: Male; Age: 52; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5209697 D5662 Peripheral blood Sex: Male; Age: 55; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5209698 D5663 Peripheral blood Sex: Male; Age: 47; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5209699 D5664 Peripheral blood Sex: Female; Age: 61; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5209700 D5665 Peripheral blood Sex: Female; Age: 29; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5209701 E04802 Peripheral blood Sex: Female; Age: 36; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5209702 E04803 Peripheral blood Sex: Female; Age: 24; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5209703 E04804 Peripheral blood Sex: Female; Age: 24; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5209704 E04805 Peripheral blood Sex: Female; Age: 21; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5209705 E04806 Peripheral blood Sex: Female; Age: 54; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5209706 E04807 Peripheral blood Sex: Female; Age: 24; Diagnosis: Healthy control Sample-local control marker detected.
Control Control GSM5209707 E04808 Peripheral blood Sex: Female; Age: 78; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209708 E04809 Peripheral blood Sex: Male; Age: 23; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209709 E04810 Peripheral blood Sex: Female; Age: 27; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209712 D5450 Peripheral blood Sex: Male; Age: 51; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209717 D5456 Peripheral blood Sex: Female; Age: 23; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209718 D5457 Peripheral blood Sex: Male; Age: 33; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209720 D5460 Peripheral blood Sex: Female; Age: 23; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209721 D5461 Peripheral blood Sex: Male; Age: 41; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209731 D5474 Peripheral blood Sex: Female; Age: 35; Diagnosis: Symptomatic control Sample-local control marker detected.
Control Control GSM5209734 D5477 Peripheral blood Sex: Female; Age: 61; Diagnosis: Symptomatic control Sample-local control marker detected.
45 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.