GSE169570

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

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

177 case / 65 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
242 samples
Specimen
Biofluid
Reported/interpreted study design
Patient biofluid vs healthy control Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Franke A, Hemmrich-Stanisak G, Juzenas S
Contact name
Simonas Juzenas
Submission date
2021-03-24
Last update
2023-01-18
Organization
Christian-Albrechts-University of Kiel
Department
Institute of Clinical Molecular Biology
Public date
2022-08-16
Experiment types
Non-coding RNA profiling by high throughput sequencing
Platforms
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA717025

Summary

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

Overall design

Total RNA extracted from peripheral blood samples (n = 242) 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
242 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

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

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 177 samples
  • Likely control group Healthy control 65 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: Patient biofluid vs healthy 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.
  • 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 860 fields

Sample Group Preview

showing 100 of 242 preview rows Show Hide
Study totals: Case 177 | Control 65 | Unassigned 0 | Excluded 0 | Ambiguous 0 showing 100 of 242 preview rows
Group Role Accession Title Source / characteristics Reason
Ulcerative colitis Case GSM5209840 C0192 Peripheral blood Sex: Female; Age: 26; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209841 C0193 Peripheral blood Sex: Male; Age: 29; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209842 C0194 Peripheral blood Sex: Female; Age: 26; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209843 C0195 Peripheral blood Sex: Male; Age: 29; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209844 C0196 Peripheral blood Sex: Female; Age: 19; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209845 C0197 Peripheral blood Sex: Male; Age: 26; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209846 C0198 Peripheral blood Sex: Female; Age: 24; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209847 C0199 Peripheral blood Sex: Female; Age: 46; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209848 C0200 Peripheral blood Sex: Female; Age: 30; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209849 C0201 Peripheral blood Sex: Male; Age: 42; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209850 C0202 Peripheral blood Sex: Female; Age: 34; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209851 C0203 Peripheral blood Sex: Female; Age: 55; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209852 C0204 Peripheral blood Sex: Female; Age: 32; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209853 C0205 Peripheral blood Sex: Male; Age: 54; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209854 C0206 Peripheral blood Sex: Male; Age: 36; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209855 C0207 Peripheral blood Sex: Male; Age: 18; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209856 C0208 Peripheral blood Sex: Male; Age: 28; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209857 C0209 Peripheral blood Sex: Female; Age: 31; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209858 C0210 Peripheral blood Sex: Female; Age: 36; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209859 C0211 Peripheral blood Sex: Male; Age: 36; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209860 C0212 Peripheral blood Sex: Female; Age: 21; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209861 C0213 Peripheral blood Sex: Male; Age: 66; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209862 C0214 Peripheral blood Sex: Female; Age: 44; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209863 C0215 Peripheral blood Sex: Male; Age: 26; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209864 C0216 Peripheral blood Sex: Female; Age: 43; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209865 C0217 Peripheral blood Sex: Female; Age: 49; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209866 C0218 Peripheral blood Sex: Male; Age: 15; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209867 C0219 Peripheral blood Sex: Female; Age: 30; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209868 C0220 Peripheral blood Sex: Male; Age: 37; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209869 C0222 Peripheral blood Sex: Male; Age: 42; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209870 C0223 Peripheral blood Sex: Male; Age: 25; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209871 C0224 Peripheral blood Sex: Female; Age: 43; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209872 C0225 Peripheral blood Sex: Male; Age: 29; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209873 C0226 Peripheral blood Sex: Female; Age: 31; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209874 C0227 Peripheral blood Sex: Female; Age: 23; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209875 C0228 Peripheral blood Sex: Female; Age: 47; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209876 C0229 Peripheral blood Sex: Male; Age: 41; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209877 C0230 Peripheral blood Sex: Male; Age: 27; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209878 C0231 Peripheral blood Sex: Male; Age: 50; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209879 C0232 Peripheral blood Sex: Male; Age: 48; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209880 C0233 Peripheral blood Sex: Female; Age: 41; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209881 C0234 Peripheral blood Sex: Female; Age: 48; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209882 C0237 Peripheral blood Sex: Female; Age: 35; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209883 C0238 Peripheral blood Sex: Male; Age: 18; Diagnosis: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM5209884 C0239 Peripheral blood Sex: Female; Age: 52; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209885 C0240 Peripheral blood Sex: Male; Age: 23; Diagnosis: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM5209886 C0241 Peripheral blood Sex: Female; Age: 45; Diagnosis: Ulcerative colitis Case marker detected.
Crohn's disease Case GSM5209887 C0242 Peripheral blood Sex: Male; Age: 31; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209888 C0243 Peripheral blood Sex: Female; Age: 46; Diagnosis: Crohn's disease Case marker detected.
Crohn's disease Case GSM5209889 C0244 Peripheral blood Sex: Female; Age: 59; Diagnosis: Crohn's disease Case marker detected.
127 additional case samples are hidden from this preview.
Healthy control Control GSM5210017 C1067 Peripheral blood Sex: Female; Age: 71; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210018 C1068 Peripheral blood Sex: Female; Age: 81; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210019 C1069 Peripheral blood Sex: Female; Age: 68; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210020 C1070 Peripheral blood Sex: Female; Age: 62; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210021 C1073 Peripheral blood Sex: Male; Age: 66; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210022 C1074 Peripheral blood Sex: Male; Age: 68; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210023 C1075 Peripheral blood Sex: Female; Age: 72; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210024 C1076 Peripheral blood Sex: Female; Age: 78; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210025 C1077 Peripheral blood Sex: Male; Age: 74; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210026 C1078 Peripheral blood Sex: Male; Age: 68; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210027 C1079 Peripheral blood Sex: Female; Age: 74; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210028 C1080 Peripheral blood Sex: Male; Age: 56; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210029 C1081 Peripheral blood Sex: Male; Age: 70; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210030 C1082 Peripheral blood Sex: Male; Age: 72; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210031 C1085 Peripheral blood Sex: Male; Age: 70; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210032 C1086 Peripheral blood Sex: Female; Age: 67; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210033 C1087 Peripheral blood Sex: Female; Age: 58; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210034 C1089 Peripheral blood Sex: Male; Age: 76; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210035 C1090 Peripheral blood Sex: Male; Age: 72; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210036 C1091 Peripheral blood Sex: Male; Age: 67; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210037 C1092 Peripheral blood Sex: Male; Age: 76; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210038 C1093 Peripheral blood Sex: Female; Age: 80; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210039 C1094 Peripheral blood Sex: Female; Age: 71; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210040 C1095 Peripheral blood Sex: Male; Age: 66; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210041 C1096 Peripheral blood Sex: Female; Age: 71; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210042 C1097 Peripheral blood Sex: Male; Age: 73; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210043 C1098 Peripheral blood Sex: Female; Age: 71; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210044 C1099 Peripheral blood Sex: Female; Age: 79; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210045 C1100 Peripheral blood Sex: Male; Age: 68; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210046 C1101 Peripheral blood Sex: Male; Age: 64; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210047 C1103 Peripheral blood Sex: Male; Age: 61; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210048 C1105 Peripheral blood Sex: Male; Age: 69; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210049 C1106 Peripheral blood Sex: Female; Age: 69; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210050 C1107 Peripheral blood Sex: Male; Age: 79; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210051 C1108 Peripheral blood Sex: Male; Age: 62; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210052 C1109 Peripheral blood Sex: Male; Age: 62; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210053 C1110 Peripheral blood Sex: Male; Age: 64; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210054 C1112 Peripheral blood Sex: Male; Age: 80; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210055 C1113 Peripheral blood Sex: Female; Age: 71; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210056 C1114 Peripheral blood Sex: Male; Age: 76; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210057 C1115 Peripheral blood Sex: Male; Age: 82; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210058 C1116 Peripheral blood Sex: Male; Age: 63; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210059 C1117 Peripheral blood Sex: Female; Age: 72; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210060 C1118 Peripheral blood Sex: Female; Age: 71; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210061 C1119 Peripheral blood Sex: Male; Age: 71; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210062 C1120 Peripheral blood Sex: Male; Age: 74; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210063 C1121 Peripheral blood Sex: Male; Age: 73; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210064 C1122 Peripheral blood Sex: Male; Age: 76; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210065 C1123 Peripheral blood Sex: Female; Age: 72; Diagnosis: Healthy control Sample-local control marker detected.
Healthy control Control GSM5210066 C1124 Peripheral blood Sex: Male; Age: 70; Diagnosis: Healthy control Sample-local control marker detected.
15 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.