GSE135223

Human macrophage responses to viral-like particles from non-IBD or IBD colonic resections

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

10 case / 8 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: 18 samples
Specimen: Unclear specimen/source
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Adiliaghdam F, Digumarthi S, Wong LP, Sadreyev R, Jeffrey KL
Contact name: Kate L Jeffrey
Submission date: 2019-08-01
Last update: 2022-08-31
Organization: Massachusetts General Hospital
Department: Medicine
Public date: 2020-06-01
Experiment types: Expression profiling by high throughput sequencing
Platforms: GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Series type: Series
SubSeries: Not available
BioProject: PRJNA557840

Summary

Peripheral blood-derived macrophages were stimulated with viral-like particles isolated from colonic resections from patients with Crohn's disease (CD), ulcerative colitis (UC), or non-IBD controls diagnoses. RNAseq was performed to unbiasedly assess the transcriptional responses to these stimuli and revealed highly divergent macrophage transcriptional programs in response to non-IBD compared to IBD VLP.

Overall design

Peripheral blood mononuclear cells from the blood of three healthy human donors were pooled and differentiated into macrophages with M-CSF over the course of seven days. Mature macrophages were treated with viral-like particle (VLP) isolates from colon resections of patients with Crohn's disease (5 individual patient samples), ulcerative colitis (5 individual patient samples), non-IBD diagnoses (5 individual patient samples), or mock treated (3 replicates of mock treatment). RNA was isolated and RNA-seq was carried out for transcriptional analysis.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 18 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 Human enteric viruses autonomously shape inflammatory bowel disease phenotype through divergent innate immunomodulation. Science immunology, 2022 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

Standard analyst review

Proceed only after the analyst confirms grouping, exclusions, and source files.

By Siftome standards, no expert review was triggered.

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 Crohn's disease 10 samples
Likely control group Mixed controls 8 samples

Intent Interpretation

Downgrade or exclusion reason Comparison: Disease/model 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, Inflammatory bowel disease, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 35394816.
Publication context: Human enteric viruses autonomously shape inflammatory bowel disease phenotype through divergent innate immunomodulation.. Science immunology, 2022. PMID 35394816. DOI 10.1126/sciimmunol.abn6660.

Cautions

Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
Downgraded for tissue search because study design or specimen source is unclear.
Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
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.
Overall score capped because comparison suitability is weak for the selected search intent.
Missing or unclear metadata. Comparison - Disease/model 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

Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.

Normalized Fields

32 fields

Field Value Source Derived by Confidence Evidence Reason

assay_type bulk RNA-seq GSE135223 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence bulk rna-seq dataset_accession: GSE135223 dataset_title: Human macrophage responses to viral-like particles from non-IBD or IBD colonic resections organism: Homo sapiens assay_type: bulk RNA... keyword match keyword match: bulk rna-seq

control_type healthy control GSM3995434 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Healthy Control rep 1 macrophage disease: Healthy Control controlled vocabulary controlled vocabulary control type match: healthy control

control_type healthy control GSM3995435 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Healthy Control rep 2 macrophage disease: Healthy Control controlled vocabulary controlled vocabulary control type match: healthy control

control_type healthy control GSM3995436 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Healthy Control rep 3 macrophage disease: Healthy Control controlled vocabulary controlled vocabulary control type match: healthy control

control_type healthy control GSM3995437 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Healthy Control rep 4 macrophage disease: Healthy Control controlled vocabulary controlled vocabulary control type match: healthy control

control_type healthy control GSM3995438 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Healthy Control rep 5 macrophage disease: Healthy Control controlled vocabulary controlled vocabulary control type match: healthy control

disease Crohn's disease GSE135223 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease dataset_accession: GSE135223 dataset_title: Human macrophage responses to viral-like particles from non-IBD or IBD colonic resections organism: Homo sapiens assay_type: bulk RNA... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease inflammatory bowel disease GSE135223 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd dataset_accession: GSE135223 dataset_title: Human macrophage responses to viral-like particles from non-IBD or IBD colonic resections organism: Homo sapiens assay_type: bulk RNA... controlled vocabulary controlled vocabulary disease match: ibd

disease ulcerative colitis GSE135223 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis dataset_accession: GSE135223 dataset_title: Human macrophage responses to viral-like particles from non-IBD or IBD colonic resections organism: Homo sapiens assay_type: bulk RNA... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease Crohn's disease GSM3995429 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Crohn's Disease rep 1 macrophage disease: Crohn's Disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM3995430 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Crohn's Disease rep 2 macrophage disease: Crohn's Disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM3995431 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Crohn's Disease rep 3 macrophage disease: Crohn's Disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM3995432 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Crohn's Disease rep 4 macrophage disease: Crohn's Disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM3995433 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Crohn's Disease rep 5 macrophage disease: Crohn's Disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease ulcerative colitis GSM3995442 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Ulcerative Colitis rep 1 macrophage disease: Ulcerative Colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM3995443 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Ulcerative Colitis rep 2 macrophage disease: Ulcerative Colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM3995444 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Ulcerative Colitis rep 3 macrophage disease: Ulcerative Colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM3995445 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Ulcerative Colitis rep 4 macrophage disease: Ulcerative Colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM3995446 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Ulcerative Colitis rep 5 macrophage disease: Ulcerative Colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

normal_tissue_type healthy donor tissue GSM3995434 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Healthy Control rep 1 macrophage disease: Healthy Control controlled vocabulary controlled vocabulary normal tissue type match: healthy control

normal_tissue_type healthy donor tissue GSM3995435 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Healthy Control rep 2 macrophage disease: Healthy Control controlled vocabulary controlled vocabulary normal tissue type match: healthy control

normal_tissue_type healthy donor tissue GSM3995436 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Healthy Control rep 3 macrophage disease: Healthy Control controlled vocabulary controlled vocabulary normal tissue type match: healthy control

normal_tissue_type healthy donor tissue GSM3995437 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Healthy Control rep 4 macrophage disease: Healthy Control controlled vocabulary controlled vocabulary normal tissue type match: healthy control

normal_tissue_type healthy donor tissue GSM3995438 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Healthy Control rep 5 macrophage disease: Healthy Control controlled vocabulary controlled vocabulary normal tissue type match: healthy control

organism Homo sapiens GSE135223 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE135223 dataset_title: Human macrophage responses to viral-like particles from non-IBD or IBD colonic resections organism: Homo sapiens assay_type: bulk RNA... keyword match keyword match: homo sapiens

sample_type normal tissue GSM3995434 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Healthy Control rep 1 macrophage disease: Healthy Control controlled vocabulary controlled vocabulary sample type match: healthy control

sample_type normal tissue GSM3995435 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Healthy Control rep 2 macrophage disease: Healthy Control controlled vocabulary controlled vocabulary sample type match: healthy control

sample_type normal tissue GSM3995436 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Healthy Control rep 3 macrophage disease: Healthy Control controlled vocabulary controlled vocabulary sample type match: healthy control

sample_type normal tissue GSM3995437 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Healthy Control rep 4 macrophage disease: Healthy Control controlled vocabulary controlled vocabulary sample type match: healthy control

sample_type normal tissue GSM3995438 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Healthy Control rep 5 macrophage disease: Healthy Control controlled vocabulary controlled vocabulary sample type match: healthy control

tissue blood GSE135223 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood dataset_accession: GSE135223 dataset_title: Human macrophage responses to viral-like particles from non-IBD or IBD colonic resections organism: Homo sapiens assay_type: bulk RNA... controlled vocabulary controlled vocabulary tissue match: blood

tissue colon GSE135223 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon dataset_accession: GSE135223 dataset_title: Human macrophage responses to viral-like particles from non-IBD or IBD colonic resections organism: Homo sapiens assay_type: bulk RNA... controlled vocabulary controlled vocabulary tissue match: colon

Sample Group Preview

18 rows shown Show Hide

Study totals: Case 10 | Control 8 | Unassigned 0 | Excluded 0 | Ambiguous 0 18 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Crohn's disease	Case	GSM3995429	Crohn's Disease rep 1	Macrophage Disease: Crohn's Disease	Case marker detected.
Crohn's disease	Case	GSM3995430	Crohn's Disease rep 2	Macrophage Disease: Crohn's Disease	Case marker detected.
Crohn's disease	Case	GSM3995431	Crohn's Disease rep 3	Macrophage Disease: Crohn's Disease	Case marker detected.
Crohn's disease	Case	GSM3995432	Crohn's Disease rep 4	Macrophage Disease: Crohn's Disease	Case marker detected.
Crohn's disease	Case	GSM3995433	Crohn's Disease rep 5	Macrophage Disease: Crohn's Disease	Case marker detected.
Ulcerative colitis	Case	GSM3995442	Ulcerative Colitis rep 1	Macrophage Disease: Ulcerative Colitis	Case marker detected.
Ulcerative colitis	Case	GSM3995443	Ulcerative Colitis rep 2	Macrophage Disease: Ulcerative Colitis	Case marker detected.
Ulcerative colitis	Case	GSM3995444	Ulcerative Colitis rep 3	Macrophage Disease: Ulcerative Colitis	Case marker detected.
Ulcerative colitis	Case	GSM3995445	Ulcerative Colitis rep 4	Macrophage Disease: Ulcerative Colitis	Case marker detected.
Ulcerative colitis	Case	GSM3995446	Ulcerative Colitis rep 5	Macrophage Disease: Ulcerative Colitis	Case marker detected.
Healthy control	Control	GSM3995434	Healthy Control rep 1	Macrophage Disease: Healthy Control	Sample-local control marker detected.
Healthy control	Control	GSM3995435	Healthy Control rep 2	Macrophage Disease: Healthy Control	Sample-local control marker detected.
Healthy control	Control	GSM3995436	Healthy Control rep 3	Macrophage Disease: Healthy Control	Sample-local control marker detected.
Healthy control	Control	GSM3995437	Healthy Control rep 4	Macrophage Disease: Healthy Control	Sample-local control marker detected.
Healthy control	Control	GSM3995438	Healthy Control rep 5	Macrophage Disease: Healthy Control	Sample-local control marker detected.
Control	Control	GSM3995439	Mock rep 1	Macrophage Disease: Mock	Sample-local control marker detected.
Control	Control	GSM3995440	Mock rep 2	Macrophage Disease: Mock	Sample-local control marker detected.
Control	Control	GSM3995441	Mock rep 3	Macrophage Disease: Mock	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.

Summary

Overall design

Source Evidence

Primary publication

Metadata Quality Components

Analysis Readiness

Blockers

Next Steps

Analysis Preparation Checklist

Bioinformatician Review

Why This Is Ranked Here

Applied Review Decisions

Derived Classifications

Intent Interpretation

Ranking Facts

Supporting evidence

Cautions

Dataset Warnings

Normalized Fields

Sample Group Preview

Use as Discovery Cohort