GSE69446

Impact of NOD2 Genotype on the Innate Monocyte Transcriptome in 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

14 case / 14 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
28 samples
Specimen
Unclear specimen/source
Reported/interpreted study design
Treatment vs control Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Nielsen OH, Seidelin JB, Sandelin A, Chen Y
Contact name
Yun Chen
Submission date
2015-06-01
Last update
2019-05-15
Organization
Chr Hansen A/S
Department
Health & Nutrition
Public date
2017-02-15
Experiment types
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA285507

Summary

Short title: Innate Gene/miRNA MDP-response in CD RNA-seq and small RNA-seq were used to identify the expression of gene and microRNA (miRNA) in monocytes from healthy controls and patients with Crohn's Disease (CD), with and without NOD2 (nucleotide-binding oligomerization domain-containing protein 2) single nucleotide polymorphisms (SNPs) after stimulation with muramyl dipeptide (MDP).

Overall design

Identification of the gene expression of mRNA and miRNA in monocytes from healthy controls and Crohn's patients with and without NOD2 SNPs before and after stimulation with the NOD2-agonist MDP.

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
28 GSM samples
 Primary source
recount3

Trusted source evidence for processed count availability.

recount3 project ID
srp058953
 Available
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. Relation between NOD2 genotype and changes in innate signaling in Crohn's disease on mRNA and miRNA levels. NPJ genomic medicine, 2017
Available

Metadata Quality Components

Persisted metadata quality

85 pts
Clarity
85%
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: Tissue metadata was not 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

Review before analysis
85% 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

3/15 pts

Unassigned or review-needed samples remain before analysis.

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

  • 14 samples need manual grouping review.
  • Secondary RNA assay context should be analyzed separately from ordinary bulk RNA-seq.

Next Steps

  • Resolve unassigned or review-needed samples in the grouping table.

Analysis Preparation Checklist

4/6 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

Needs review

14 review-needed samples and 0 unassigned samples remain.

Resolve ambiguous and unassigned samples before finalizing the contrast.

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.

One or more samples were flagged for manual review.

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 Disease context came from Normalization rules.
  • Likely case group Treated 14 samples
  • Likely control group Untreated 14 samples

Intent Interpretation

  • Downgrade or exclusion reason Comparison: Treatment vs control. Specimen: Unclear specimen/source. 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.
  • Processed data is available for downstream review.
  • External evidence: recount3 reports trusted processed count availability.
  • External evidence: PubMed links 1 publication; 1 DOI available: PMID 29263823.
  • Publication context: Relation between NOD2 genotype and changes in innate signaling in Crohn's disease on mRNA and miRNA levels.. NPJ genomic medicine, 2017. PMID 29263823. DOI 10.1038/s41525-016-0001-4.

Cautions

  • Comparison: Treatment vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
  • Downgraded for tissue search because it is a treatment/control experiment.
  • Downgraded for tissue search because study design or specimen source is unclear.
  • Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons.
  • Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
  • Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
  • Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
  • Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
  • 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.
  • Missing or unclear metadata. Comparison - Treatment vs control. Specimen - Unclear specimen/source. 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

91 fields

Sample Group Preview

28 rows shown Show Hide
Study totals: Case 14 | Control 14 | Unassigned 0 | Excluded 0 | Ambiguous 0 28 rows shown
Group Role Accession Title Source / characteristics Reason
Treated Case GSM1701327 RNA-seq CD NOD2 after MDP, replicate1 Monocytes, CD, NOD2 SNP, stimulated with MDP Cell type: Monocytes; Disease status: Crohn's disease; Genotype: HOM SNP13 + WT ATG16L1; Treatment: Stimulated with muramyl dipeptide (MDP) treated sample: Treated sample may need exclusion outside treatment comparisons.
Treated Case GSM1701328 RNA-seq CD NOD2 after MDP, replicate2 Monocytes, CD, NOD2 SNP, stimulated with MDP Cell type: Monocytes; Disease status: Crohn's disease; Genotype: HET SNP13/HET SNP12 + WT ATG16L1; Treatment: Stimulated with muramyl dipeptide (MDP) treated sample: Treated sample may need exclusion outside treatment comparisons.
Treated Case GSM1701329 RNA-seq CD NOD2 after MDP, replicate3 Monocytes, CD, NOD2 SNP, stimulated with MDP Cell type: Monocytes; Disease status: Crohn's disease; Genotype: HET SNP13/HET SNP8 + WT ATG16L1; Treatment: Stimulated with muramyl dipeptide (MDP) treated sample: Treated sample may need exclusion outside treatment comparisons.
Treated Case GSM1701333 RNA-seq CD WT after MDP, replicate1 Monocytes, CD, WT, stimulated with MDP Cell type: Monocytes; Disease status: Crohn's disease; Genotype: WT NOD2 + WT ATG16L1; Treatment: Stimulated with muramyl dipeptide (MDP) treated sample: Treated sample may need exclusion outside treatment comparisons.
Treated Case GSM1701334 RNA-seq CD WT after MDP, replicate2 Monocytes, CD, WT, stimulated with MDP Cell type: Monocytes; Disease status: Crohn's disease; Genotype: WT NOD2 + WT ATG16L1; Treatment: Stimulated with muramyl dipeptide (MDP) treated sample: Treated sample may need exclusion outside treatment comparisons.
Treated Case GSM1701337 RNA-seq healthy control after MDP, replicate1 Monocytes, healthy, WT, stimulated with MDP Cell type: Monocytes; Disease status: Healthy; Genotype: WT NOD2 + WT ATG16L1; Treatment: Stimulated with muramyl dipeptide (MDP) treated sample: Treated sample may need exclusion outside treatment comparisons.
Treated Case GSM1701338 RNA-seq healthy control after MDP, replicate2 Monocytes, healthy, WT, stimulated with MDP Cell type: Monocytes; Disease status: Healthy; Genotype: WT NOD2 + WT ATG16L1; Treatment: Stimulated with muramyl dipeptide (MDP) treated sample: Treated sample may need exclusion outside treatment comparisons.
Treated Case GSM1701341 Small RNA-seq CD NOD2 after MDP, replicate1 Monocytes, CD, NOD2 SNP, stimulated with MDP Cell type: Monocytes; Disease status: Crohn's disease; Genotype: HOM SNP13 + WT ATG16L1; Treatment: Stimulated with muramyl dipeptide (MDP) treated sample: Treated sample may need exclusion outside treatment comparisons.
Treated Case GSM1701342 Small RNA-seq CD NOD2 after MDP, replicate2 Monocytes, CD, NOD2 SNP, stimulated with MDP Cell type: Monocytes; Disease status: Crohn's disease; Genotype: HET SNP13/HET SNP12 + WT ATG16L1; Treatment: Stimulated with muramyl dipeptide (MDP) treated sample: Treated sample may need exclusion outside treatment comparisons.
Treated Case GSM1701343 Small RNA-seq CD NOD2 after MDP, replicate3 Monocytes, CD, NOD2 SNP, stimulated with MDP Cell type: Monocytes; Disease status: Crohn's disease; Genotype: HET SNP13/HET SNP8 + WT ATG16L1; Treatment: Stimulated with muramyl dipeptide (MDP) treated sample: Treated sample may need exclusion outside treatment comparisons.
Treated Case GSM1701347 Small RNA-seq CD WT after MDP, replicate1 Monocytes, CD, WT, stimulated with MDP Cell type: Monocytes; Disease status: Crohn's disease; Genotype: WT NOD2 + WT ATG16L1; Treatment: Stimulated with muramyl dipeptide (MDP) treated sample: Treated sample may need exclusion outside treatment comparisons.
Treated Case GSM1701348 Small RNA-seq CD WT after MDP, replicate2 Monocytes, CD, WT, stimulated with MDP Cell type: Monocytes; Disease status: Crohn's disease; Genotype: WT NOD2 + WT ATG16L1; Treatment: Stimulated with muramyl dipeptide (MDP) treated sample: Treated sample may need exclusion outside treatment comparisons.
Treated Case GSM1701351 Small RNA-seq ctrl_after MDP, replicate1 Monocytes, healthy, WT, stimulated with MDP Cell type: Monocytes; Disease status: Healthy; Genotype: WT NOD2 + WT ATG16L1; Treatment: Stimulated with muramyl dipeptide (MDP) treated sample: Treated sample may need exclusion outside treatment comparisons.
Treated Case GSM1701352 Small RNA-seq ctrl_after MDP, replicate2 Monocytes, healthy, WT, stimulated with MDP Cell type: Monocytes; Disease status: Healthy; Genotype: WT NOD2 + WT ATG16L1; Treatment: Stimulated with muramyl dipeptide (MDP) treated sample: Treated sample may need exclusion outside treatment comparisons.
Untreated Control GSM1701330 RNA-seq CD NOD2 before MDP, replicate1 Monocytes, CD, NOD2 SNP, unstimulated Cell type: Monocytes; Disease status: Crohn's disease; Genotype: HOM SNP13 + WT ATG16L1; Treatment: Unstimulated Treatment control marker detected.
Untreated Control GSM1701331 RNA-seq CD NOD2 before MDP, replicate2 Monocytes, CD, NOD2 SNP, unstimulated Cell type: Monocytes; Disease status: Crohn's disease; Genotype: HET SNP13/HET SNP12 + WT ATG16L1; Treatment: Unstimulated Treatment control marker detected.
Untreated Control GSM1701332 RNA-seq CD NOD2 before MDP, replicate3 Monocytes, CD, NOD2 SNP, unstimulated Cell type: Monocytes; Disease status: Crohn's disease; Genotype: HET SNP13/HET SNP8 + WT ATG16L1; Treatment: Unstimulated Treatment control marker detected.
Untreated Control GSM1701335 RNA-seq CD WT before MDP, replicate1 Monocytes, CD, WT, unstimulated Cell type: Monocytes; Disease status: Crohn's disease; Genotype: WT NOD2 + WT ATG16L1; Treatment: Unstimulated Treatment control marker detected.
Untreated Control GSM1701336 RNA-seq CD WT before MDP, replicate2 Monocytes, CD, WT, unstimulated Cell type: Monocytes; Disease status: Crohn's disease; Genotype: WT NOD2 + WT ATG16L1; Treatment: Unstimulated Treatment control marker detected.
Untreated Control GSM1701339 RNA-seq healthy control before MDP, replicate1 Monocytes, healthy, WT, unstimulated Cell type: Monocytes; Disease status: Healthy; Genotype: WT NOD2 + WT ATG16L1; Treatment: Unstimulated Treatment control marker detected.
Untreated Control GSM1701340 RNA-seq healthy control before MDP, replicate2 Monocytes, healthy, WT, unstimulated Cell type: Monocytes; Disease status: Healthy; Genotype: WT NOD2 + WT ATG16L1; Treatment: Unstimulated Treatment control marker detected.
Untreated Control GSM1701344 Small RNA-seq CD NOD2 before MDP, replicate1 Monocytes, CD, NOD2 SNP, unstimulated Cell type: Monocytes; Disease status: Crohn's disease; Genotype: HOM SNP13 + WT ATG16L1; Treatment: Unstimulated Treatment control marker detected.
Untreated Control GSM1701345 Small RNA-seq CD NOD2 before MDP, replicate2 Monocytes, CD, NOD2 SNP, unstimulated Cell type: Monocytes; Disease status: Crohn's disease; Genotype: HET SNP13/HET SNP12 + WT ATG16L1; Treatment: Unstimulated Treatment control marker detected.
Untreated Control GSM1701346 Small RNA-seq CD NOD2 before MDP, replicate3 Monocytes, CD, NOD2 SNP, unstimulated Cell type: Monocytes; Disease status: Crohn's disease; Genotype: HET SNP13/HET SNP8 + WT ATG16L1; Treatment: Unstimulated Treatment control marker detected.
Untreated Control GSM1701349 Small RNA-seq CD WT before MDP, replicate1 Monocytes, CD, WT, unstimulated Cell type: Monocytes; Disease status: Crohn's disease; Genotype: WT NOD2 + WT ATG16L1; Treatment: Unstimulated Treatment control marker detected.
Untreated Control GSM1701350 Small RNA-seq CD WT before MDP, replicate2 Monocytes, CD, WT, unstimulated Cell type: Monocytes; Disease status: Crohn's disease; Genotype: WT NOD2 + WT ATG16L1; Treatment: Unstimulated Treatment control marker detected.
Untreated Control GSM1701353 Small RNA-seq ctrl_before MDP, replicate1 Monocytes, healthy, WT, unstimulated Cell type: Monocytes; Disease status: Healthy; Genotype: WT NOD2 + WT ATG16L1; Treatment: Unstimulated Treatment control marker detected.
Untreated Control GSM1701354 Small RNA-seq ctrl_before MDP, replicate2 Monocytes, healthy, WT, unstimulated Cell type: Monocytes; Disease status: Healthy; Genotype: WT NOD2 + WT ATG16L1; Treatment: Unstimulated Treatment control marker detected.

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.