GSE110186

NOD2- and disease-specific gene expression profiles of peripheral blood mononuclear cells from Crohn’s disease patients

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

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: microarray
Organism: Homo sapiens
Whole-study samples: 24 samples
Specimen: Biofluid
Reported/interpreted study design: Treatment vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Schäffler H, Rohde M, Rohde S, Huth A, Gittel N, Hollborn H, Koczan D, Glass Ä, Lamprecht G, Jaster R
Contact name: Dirk Koczan
Submission date: 2018-02-06
Last update: 2019-02-01
Organization: University of Rostock
Department: Institute for Immunology
Public date: 2018-04-03
Experiment types: Expression profiling by array
Platforms: GPL23159 [Clariom_S_Human] Affymetrix Clariom S Assay, Human (Includes Pico Assay)
Series type: Series
SubSeries: Not available
BioProject: PRJNA433092

Summary

Employing microarray assays, a total of 267 genes were identified that were significantly up- or downregulated in PBMCs of WT-NOD2 patients, compared to healthy donors after challenge with vitamin D (+/-D) and/or a combination (+/-LP) of LPS (lipopolysaccharide) and PGN (peptidoglycan) (p < 0.05; threshold: ≥ 2-fold change). For further analysis by real-time PCR, 12 genes with known impact on inflammation and immunity were selected that fulfilled predefined expression criteria. In a larger cohort of patients and controls, a disease-associated expression pattern, with higher transcript levels in vitamin D-treated PBMCs from 5 patients, was observed for three of these genes, CLEC5A (p < 0.030), lysozyme (LYZ; p < 0.047) and TREM1 (p < 0.023). Six genes were found to be expressed in a NOD2- dependent manner (CD101, p < 0.002; CLEC5A, p < 0.020; CXCL5, p < 0.009; IL-24, p < 0.044; ITGB2, p < 0.041; LYZ, p < 0.042). Interestingly, the highest transcript levels were observed in patients with heterozygous NOD2 mutations.

Overall design

PBMC`s of 3 patient and 3 controls were treated with vitamin D and/or a combination of LPS and PGN resulting in 8 triplicates (24 hybridization samples)

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 24 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 NOD2- and disease-specific gene expression profiles of peripheral blood mononuclear cells from Crohn's disease patients. World journal of gastroenterology, 2018 PubMed DOI	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

Ready after review

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

No readiness blockers detected.

Next Steps

Verify the proposed sample assignments and case-versus-control comparison against the GEO metadata before using them in DESeq2 or another differential-expression tool.
Confirm processed count files and sample identifiers match the exported metadata.

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.

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

Assay differs from search intent Microarray Search intent expects bulk RNA-seq. Assay came from Normalization rules.
Disease context Crohn's disease Disease context came from Normalization rules.
Likely case group Treated 18 samples
Likely control group Healthy control 6 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: Treatment vs control. Specimen: Biofluid. Comparison suitability: 0%.
Interpreted disease metadata: Crohn's disease.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 29568200.
Publication context: NOD2- and disease-specific gene expression profiles of peripheral blood mononuclear cells from Crohn's disease patients.. World journal of gastroenterology, 2018. PMID 29568200. DOI 10.3748/wjg.v24.i11.1196.

Cautions

Downgraded for tissue search because it is a biofluid cohort.
Downgraded for tissue search because it is a treatment/control experiment.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons.
Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
Overall score capped because comparison suitability is weak for the selected search intent.
Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Microarray expression context was detected; compare separately from RNA-seq cohorts.
Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.

Normalized Fields

172 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source blood GSM2981862 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981863 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981864 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981865 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981866 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981867 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981868 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981869 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981870 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981871 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981872 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981873 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981874 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981875 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981876 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981877 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981878 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981879 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981880 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981881 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981882 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981883 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981884 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2981885 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE110186 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE110186 dataset_title: NOD2- and disease-specific gene expression profiles of peripheral blood mononuclear cells from Crohn’s disease patients organism: Hom... keyword match keyword match: microarray

cell_population peripheral blood mononuclear cells GSM2981862 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_1_+D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981863 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_2_+D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981864 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_3_+D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981865 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_1_+D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981866 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_2_+D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981867 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_3_+D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981868 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_1_-D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981869 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_2_-D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981870 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_3_-D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981871 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_1_-D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: none controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981872 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_2_-D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: none controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981873 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_3_-D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: none controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981874 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_1_+D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981875 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_2_+D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981876 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_3_+D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981877 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_1_+D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981878 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_2_+D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981879 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_3_+D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981880 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_1_-D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981881 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_2_-D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981882 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_3_-D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981883 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_1_-D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: none controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981884 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_2_-D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: none controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2981885 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_3_-D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: none controlled vocabulary controlled vocabulary cell population match: pbmc

control_type healthy control GSM2981862 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_1_+D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary control type match: healthy donor

control_type healthy control GSM2981863 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_2_+D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary control type match: healthy donor

control_type healthy control GSM2981864 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_3_+D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary control type match: healthy donor

control_type healthy control GSM2981865 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_1_+D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D controlled vocabulary controlled vocabulary control type match: healthy donor

control_type healthy control GSM2981866 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_2_+D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D controlled vocabulary controlled vocabulary control type match: healthy donor

control_type healthy control GSM2981867 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_3_+D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D controlled vocabulary controlled vocabulary control type match: healthy donor

control_type healthy control GSM2981868 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_1_-D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary control type match: healthy donor

control_type healthy control GSM2981869 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_2_-D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary control type match: healthy donor

control_type healthy control GSM2981870 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_3_-D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary control type match: healthy donor

control_type healthy control GSM2981871 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_1_-D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: none controlled vocabulary controlled vocabulary control type match: healthy donor

control_type healthy control GSM2981872 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_2_-D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: none controlled vocabulary controlled vocabulary control type match: healthy donor

control_type healthy control GSM2981873 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_3_-D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: none controlled vocabulary controlled vocabulary control type match: healthy donor

disease Crohn's disease GSE110186 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease dataset_accession: GSE110186 dataset_title: NOD2- and disease-specific gene expression profiles of peripheral blood mononuclear cells from Crohn’s disease patients organism: Hom... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2981874 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Patient_1_+D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2981875 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Patient_2_+D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2981876 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Patient_3_+D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2981877 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Patient_1_+D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2981878 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Patient_2_+D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2981879 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Patient_3_+D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2981880 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Patient_1_-D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2981881 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Patient_2_-D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2981882 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Patient_3_-D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2981883 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Patient_1_-D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: none controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2981884 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Patient_2_-D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: none controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2981885 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Patient_3_-D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: none controlled vocabulary controlled vocabulary disease match: Crohn's disease

normal_tissue_type healthy donor tissue GSM2981862 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_1_+D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary normal tissue type match: healthy donor

normal_tissue_type healthy donor tissue GSM2981863 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_2_+D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary normal tissue type match: healthy donor

normal_tissue_type healthy donor tissue GSM2981864 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_3_+D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary normal tissue type match: healthy donor

normal_tissue_type healthy donor tissue GSM2981865 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_1_+D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D controlled vocabulary controlled vocabulary normal tissue type match: healthy donor

normal_tissue_type healthy donor tissue GSM2981866 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_2_+D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D controlled vocabulary controlled vocabulary normal tissue type match: healthy donor

normal_tissue_type healthy donor tissue GSM2981867 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_3_+D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D controlled vocabulary controlled vocabulary normal tissue type match: healthy donor

normal_tissue_type healthy donor tissue GSM2981868 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_1_-D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary normal tissue type match: healthy donor

normal_tissue_type healthy donor tissue GSM2981869 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_2_-D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary normal tissue type match: healthy donor

normal_tissue_type healthy donor tissue GSM2981870 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_3_-D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary normal tissue type match: healthy donor

normal_tissue_type healthy donor tissue GSM2981871 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_1_-D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: none controlled vocabulary controlled vocabulary normal tissue type match: healthy donor

normal_tissue_type healthy donor tissue GSM2981872 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_2_-D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: none controlled vocabulary controlled vocabulary normal tissue type match: healthy donor

normal_tissue_type healthy donor tissue GSM2981873 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_3_-D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: none controlled vocabulary controlled vocabulary normal tissue type match: healthy donor

organism Homo sapiens GSE110186 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE110186 dataset_title: NOD2- and disease-specific gene expression profiles of peripheral blood mononuclear cells from Crohn’s disease patients organism: Hom... keyword match keyword match: homo sapiens

preparation_process density-gradient isolation GSM2981862 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Control_1_+D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981863 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Control_2_+D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981864 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Control_3_+D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981865 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Control_1_+D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981866 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Control_2_+D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981867 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Control_3_+D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981868 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Control_1_-D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981869 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Control_2_-D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981870 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Control_3_-D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981871 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Control_1_-D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: none controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981872 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Control_2_-D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: none controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981873 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Control_3_-D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: none controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981874 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Patient_1_+D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981875 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Patient_2_+D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981876 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Patient_3_+D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981877 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Patient_1_+D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981878 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Patient_2_+D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981879 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Patient_3_+D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981880 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Patient_1_-D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981881 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Patient_2_-D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981882 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Patient_3_-D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981883 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Patient_1_-D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: none controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981884 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Patient_2_-D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: none controlled vocabulary controlled vocabulary preparation process match: density-gradient

preparation_process density-gradient isolation GSM2981885 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence density-gradient Patient_3_-D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: none controlled vocabulary controlled vocabulary preparation process match: density-gradient

sample_type normal tissue GSM2981862 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_1_+D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary sample type match: healthy donor

sample_type normal tissue GSM2981863 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_2_+D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary sample type match: healthy donor

sample_type normal tissue GSM2981864 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_3_+D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary sample type match: healthy donor

sample_type normal tissue GSM2981865 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_1_+D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D controlled vocabulary controlled vocabulary sample type match: healthy donor

sample_type normal tissue GSM2981866 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_2_+D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D controlled vocabulary controlled vocabulary sample type match: healthy donor

sample_type normal tissue GSM2981867 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_3_+D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D controlled vocabulary controlled vocabulary sample type match: healthy donor

sample_type normal tissue GSM2981868 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_1_-D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary sample type match: healthy donor

sample_type normal tissue GSM2981869 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_2_-D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary sample type match: healthy donor

sample_type normal tissue GSM2981870 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_3_-D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary sample type match: healthy donor

sample_type normal tissue GSM2981871 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_1_-D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: none controlled vocabulary controlled vocabulary sample type match: healthy donor

sample_type normal tissue GSM2981872 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_2_-D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: none controlled vocabulary controlled vocabulary sample type match: healthy donor

sample_type normal tissue GSM2981873 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy donor Control_3_-D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: none controlled vocabulary controlled vocabulary sample type match: healthy donor

specimen_material PBMC preparation GSM2981862 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_1_+D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981863 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_2_+D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981864 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_3_+D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981865 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_1_+D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981866 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_2_+D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981867 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_3_+D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981868 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_1_-D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981869 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_2_-D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981870 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_3_-D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981871 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_1_-D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: none controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981872 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_2_-D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: none controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981873 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_3_-D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: none controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981874 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_1_+D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981875 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_2_+D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981876 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_3_+D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981877 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_1_+D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981878 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_2_+D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981879 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_3_+D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981880 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_1_-D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981881 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_2_-D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981882 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_3_-D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981883 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_1_-D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: none controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981884 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_2_-D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: none controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2981885 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_3_-D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: none controlled vocabulary controlled vocabulary specimen material match: pbmc

tissue blood GSE110186 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood dataset_accession: GSE110186 dataset_title: NOD2- and disease-specific gene expression profiles of peripheral blood mononuclear cells from Crohn’s disease patients organism: Hom... controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2981862 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_1_+D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981863 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_2_+D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981864 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_3_+D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981865 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_1_+D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981866 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_2_+D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981867 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_3_+D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: Vitamin D controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981868 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_1_-D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981869 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_2_-D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981870 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_3_-D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981871 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_1_-D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: none controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981872 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_2_-D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: none controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981873 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Control_3_-D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: healthy donor; treatment: none controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981874 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_1_+D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981875 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_2_+D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981876 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_3_+D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D/lipopolysaccharide/peptidoglycan controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981877 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_1_+D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981878 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_2_+D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981879 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_3_+D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: Vitamin D controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981880 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_1_-D+LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981881 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_2_-D+LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981882 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_3_-D+LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: lipopolysaccharide and peptidoglycan controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981883 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_1_-D-LP, biological replicate 1 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: none controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981884 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_2_-D-LP, biological replicate 2 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: none controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM2981885 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Patient_3_-D-LP, biological replicate 3 PBMCs by density-gradient centrifugation tissue: PBMC; disease state: Crohn’s disease; treatment: none controlled vocabulary controlled vocabulary tissue match: pbmc

Sample Group Preview

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Study totals: Case 18 | Control 6 | Unassigned 0 | Excluded 0 | Ambiguous 0 24 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Treated	Case	GSM2981862	Control_1_+D+LP, biological replicate 1	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Healthy donor; Treatment: Vitamin D/lipopolysaccharide/peptidoglycan	Treatment case marker detected.
Treated	Case	GSM2981863	Control_2_+D+LP, biological replicate 2	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Healthy donor; Treatment: Vitamin D/lipopolysaccharide/peptidoglycan	Treatment case marker detected.
Treated	Case	GSM2981864	Control_3_+D+LP, biological replicate 3	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Healthy donor; Treatment: Vitamin D/lipopolysaccharide/peptidoglycan	Treatment case marker detected.
Treated	Case	GSM2981868	Control_1_-D+LP, biological replicate 1	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Healthy donor; Treatment: Lipopolysaccharide and peptidoglycan	Treatment case marker detected.
Treated	Case	GSM2981869	Control_2_-D+LP, biological replicate 2	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Healthy donor; Treatment: Lipopolysaccharide and peptidoglycan	Treatment case marker detected.
Treated	Case	GSM2981870	Control_3_-D+LP, biological replicate 3	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Healthy donor; Treatment: Lipopolysaccharide and peptidoglycan	Treatment case marker detected.
Treated	Case	GSM2981874	Patient_1_+D+LP, biological replicate 1	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Crohn’s disease; Treatment: Vitamin D/lipopolysaccharide/peptidoglycan	Treatment case marker detected.
Treated	Case	GSM2981875	Patient_2_+D+LP, biological replicate 2	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Crohn’s disease; Treatment: Vitamin D/lipopolysaccharide/peptidoglycan	Treatment case marker detected.
Treated	Case	GSM2981876	Patient_3_+D+LP, biological replicate 3	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Crohn’s disease; Treatment: Vitamin D/lipopolysaccharide/peptidoglycan	Treatment case marker detected.
Crohn's disease	Case	GSM2981877	Patient_1_+D-LP, biological replicate 1	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Crohn’s disease; Treatment: Vitamin D	Case marker detected.
Crohn's disease	Case	GSM2981878	Patient_2_+D-LP, biological replicate 2	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Crohn’s disease; Treatment: Vitamin D	Case marker detected.
Crohn's disease	Case	GSM2981879	Patient_3_+D-LP, biological replicate 3	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Crohn’s disease; Treatment: Vitamin D	Case marker detected.
Treated	Case	GSM2981880	Patient_1_-D+LP, biological replicate 1	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Crohn’s disease; Treatment: Lipopolysaccharide and peptidoglycan	Treatment case marker detected.
Treated	Case	GSM2981881	Patient_2_-D+LP, biological replicate 2	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Crohn’s disease; Treatment: Lipopolysaccharide and peptidoglycan	Treatment case marker detected.
Treated	Case	GSM2981882	Patient_3_-D+LP, biological replicate 3	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Crohn’s disease; Treatment: Lipopolysaccharide and peptidoglycan	Treatment case marker detected.
Crohn's disease	Case	GSM2981883	Patient_1_-D-LP, biological replicate 1	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Crohn’s disease; Treatment: None	Case marker detected.
Crohn's disease	Case	GSM2981884	Patient_2_-D-LP, biological replicate 2	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Crohn’s disease; Treatment: None	Case marker detected.
Crohn's disease	Case	GSM2981885	Patient_3_-D-LP, biological replicate 3	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Crohn’s disease; Treatment: None	Case marker detected.
Healthy control	Control	GSM2981865	Control_1_+D-LP, biological replicate 1	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Healthy donor; Treatment: Vitamin D	Sample-local control marker detected.
Healthy control	Control	GSM2981866	Control_2_+D-LP, biological replicate 2	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Healthy donor; Treatment: Vitamin D	Sample-local control marker detected.
Healthy control	Control	GSM2981867	Control_3_+D-LP, biological replicate 3	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Healthy donor; Treatment: Vitamin D	Sample-local control marker detected.
Healthy control	Control	GSM2981871	Control_1_-D-LP, biological replicate 1	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Healthy donor; Treatment: None	Sample-local control marker detected.
Healthy control	Control	GSM2981872	Control_2_-D-LP, biological replicate 2	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Healthy donor; Treatment: None	Sample-local control marker detected.
Healthy control	Control	GSM2981873	Control_3_-D-LP, biological replicate 3	PBMCs by density-gradient centrifugation Tissue: PBMC; Disease state: Healthy donor; Treatment: None	Sample-local 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.

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Use as Discovery Cohort