GSE148233

Macrophages in Crohn’s disease creeping fat are predominantly inflammatory and produce calprotectin

Whole-study status Not suitable

Dataset does not meet the current suitability threshold.

Whole-study downloads — these do not apply your sample requirements.

Selected cohort requirements

Samples meeting selected requirements: 0 cases / 0 controls

View matching samples

14 case / 0 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: microarray
Organism: Homo sapiens
Whole-study samples: 22 samples
Specimen: Unclear specimen/source
Reported/interpreted study design: Unclear study design Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Wildenberg ME, Bloemendaal FM, Wildenberg M
Contact name: Manon Wildenberg
Submission date: 2020-04-07
Last update: 2021-04-10
Organization: Amsterdam UMC
Department: Gastroenterology
Public date: 2021-04-07
Experiment types: Expression profiling by array
Platforms: GPL24324 [Clariom_S_Human_HT] Affymetrix Clariom S Assay HT, Human (Includes Pico Assay)
Series type: Series
SubSeries: Not available
BioProject: PRJNA623563

Summary

Crohn’s disease is characterized by transmural inflammation and therefore the mesenteric immune compartment has gained interest. However, its significance in Crohn’s disease is largely unclear. Macrophages are plastic cells that adapt their phenotype to environmental stimuli resulting in inflammatory and regulatory macrophage subsets. Hence, their distribution can reflect the overall nature of an immune infiltrate. We show that mesenteric macrophages contain two populations, characterized as CD11b-high and CD11b-dim. The CD11b-dim population is characterized by expression of regulatory markers CD206, CD200R, CD163, PD-L2, CD32. CD11b-high macrophages display an IFNγ induced signature and produce high levels of calprotectin. CD11b-dim and CD11b-high populations were comparable between Crohn’s disease and other indications in expression pattern, but the CD11b-high population was strongly overrepresented in this patient group.

Overall design

CD11b-high macrophages were isolated from the mesentery of patients undergoing bowel resection (n=12). CD11b-low macrophages were isolated from the same patients (n=10, remaining patients did not yield sufficient number of cells).

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 22 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	Publication context when PubMed identifiers are already known.	No match found

Metadata Quality Components

Persisted metadata quality

78 pts

Clarity: 78%
Weight: 100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Only one side of the comparison is clearly grouped. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Tissue metadata was not 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

Not ready

40% DE readiness

Contrast completeness

10/25 pts

Only one side of the contrast is present; downstream DE needs both groups.

Minimum group size

0/20 pts

Minimum group size cannot be evaluated until a complete contrast exists.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

3/15 pts

Unassigned or review-needed samples remain before analysis.

Blocking warnings

0/10 pts

Critical warnings must be resolved before downstream analysis.

Metadata normalization

7/10 pts

Metadata quality is usable, but still deserves review.

Blockers

No complete case/control contrast is available.
8 samples are still unassigned.
Critical dataset warnings must be resolved.

Next Steps

Resolve unassigned or review-needed samples in the grouping table.
Resolve critical warnings before downstream analysis.

Analysis Preparation Checklist

3/6 ready

Group labels reviewed

Blocked

No complete case/control grouping exists yet.

Review the sample grouping table and assign both case and control groups.

Minimum sample count met

Blocked

At least one group has fewer than 2 samples.

Choose a larger dataset or merge only scientifically valid groups.

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

Verify that downloaded processed files contain usable count or expression identifiers.

Ambiguous samples handled

Needs review

0 review-needed samples and 8 unassigned samples remain.

Resolve ambiguous and unassigned samples before finalizing the contrast.

Exclusion decisions recorded

Ready

No hard-excluded samples were detected by the current rules.

Record any manual exclusions in the downstream analysis notes.

Source traceability preserved

Ready

The dataset and sample accessions can be traced back to GEO.

Keep GEO accessions with exported metadata.

Bioinformatician Review

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.

Analysis readiness has blockers that must be resolved before DE.

Analysis preparation checklist contains blocked items.

No complete case/control or treatment/control contrast is available.

At least one comparison group has fewer than two samples.

One or more samples are unassigned and need manual grouping decisions.

Critical dataset warnings are present.

Assay context may require expert handling before DESeq2-style analysis.

Study design is model-system or unclear and should be reviewed before 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, ulcerative colitis Disease context came from Normalization rules.
Likely case group Ulcerative colitis 14 samples
Likely control group No control group detected 0 samples

Intent Interpretation

Downgrade or exclusion reason Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

Interpreted disease metadata: Crohn's disease, Ulcerative colitis.
Processed data is available for downstream review.

Cautions

Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%.
Downgraded for tissue search because study design or specimen source is unclear.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
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.
Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
Overall score capped because comparison suitability is weak for the selected search intent.
Missing or unclear metadata. Comparison - Unclear study design. 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

No clear control group was detected from normalized metadata.
Microarray expression context was detected; compare separately from RNA-seq cohorts.
Tissue or cell type could not be normalized.
Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
Patient-tissue tumor-normal intent requires clear tumor-normal grouping.
Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.

Normalized Fields

17 fields

Field Value Source Derived by Confidence Evidence Reason

assay_type microarray GSE148233 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE148233 dataset_title: Macrophages in Crohn’s disease creeping fat are predominantly inflammatory and produce calprotectin organism: Homo sapiens assay_type... keyword match keyword match: microarray

disease Crohn's disease GSE148233 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease dataset_accession: GSE148233 dataset_title: Macrophages in Crohn’s disease creeping fat are predominantly inflammatory and produce calprotectin organism: Homo sapiens assay_type... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease ulcerative colitis GSM4456468 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis NonCD1_Dim Mesentery, macrophage, CD11b Dim, Ulcerative colitis cell type: macrophage; cd11b population: Dim; diagnosis: Ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM4456469 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis NonCD1_High Mesentery, macrophage, CD11b High, Ulcerative colitis cell type: macrophage; cd11b population: High; diagnosis: Ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease Crohn's disease GSM4456470 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD1_High Mesentery, macrophage, CD11b High, Crohn cell type: macrophage; cd11b population: High; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM4456473 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD2_High Mesentery, macrophage, CD11b High, Crohn cell type: macrophage; cd11b population: High; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM4456474 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD3_Dim Mesentery, macrophage, CD11b Dim, Crohn cell type: macrophage; cd11b population: Dim; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM4456475 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD3_High Mesentery, macrophage, CD11b High, Crohn cell type: macrophage; cd11b population: High; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease ulcerative colitis GSM4456476 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis NonCD3_Dim Mesentery, macrophage, CD11b Dim, Ulcerative colitis cell type: macrophage; cd11b population: Dim; diagnosis: Ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM4456477 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis NonCD3_High Mesentery, macrophage, CD11b High, Ulcerative colitis cell type: macrophage; cd11b population: High; diagnosis: Ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease Crohn's disease GSM4456478 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD4_Dim Mesentery, macrophage, CD11b Dim, Crohn cell type: macrophage; cd11b population: Dim; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM4456479 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD4_High Mesentery, macrophage, CD11b High, Crohn cell type: macrophage; cd11b population: High; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM4456480 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD5_Dim Mesentery, macrophage, CD11b Dim, Crohn cell type: macrophage; cd11b population: Dim; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM4456481 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD5_High Mesentery, macrophage, CD11b High, Crohn cell type: macrophage; cd11b population: High; diagnosis: Crohn's disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease ulcerative colitis GSM4456484 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis NonCD5_Dim Mesentery, macrophage, CD11b Dim, Ulcerative colitis cell type: macrophage; cd11b population: Dim; diagnosis: Ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM4456485 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis NonCD5_High Mesentery, macrophage, CD11b High, Ulcerative colitis cell type: macrophage; cd11b population: High; diagnosis: Ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

organism Homo sapiens GSE148233 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE148233 dataset_title: Macrophages in Crohn’s disease creeping fat are predominantly inflammatory and produce calprotectin organism: Homo sapiens assay_type... keyword match keyword match: homo sapiens

Sample Group Preview

22 rows shown Show Hide

Study totals: Case 14 | Control 0 | Unassigned 8 | Excluded 0 | Ambiguous 0 22 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Ulcerative colitis	Case	GSM4456468	NonCD1_Dim	Mesentery, macrophage, CD11b Dim, Ulcerative colitis Cell type: Macrophage; Cd11b population: Dim; Diagnosis: Ulcerative colitis	Case marker detected.
Ulcerative colitis	Case	GSM4456469	NonCD1_High	Mesentery, macrophage, CD11b High, Ulcerative colitis Cell type: Macrophage; Cd11b population: High; Diagnosis: Ulcerative colitis	Case marker detected.
Crohn's disease	Case	GSM4456470	CD1_High	Mesentery, macrophage, CD11b High, Crohn Cell type: Macrophage; Cd11b population: High; Diagnosis: Crohn's disease	Case marker detected.
Crohn's disease	Case	GSM4456473	CD2_High	Mesentery, macrophage, CD11b High, Crohn Cell type: Macrophage; Cd11b population: High; Diagnosis: Crohn's disease	Case marker detected.
Crohn's disease	Case	GSM4456474	CD3_Dim	Mesentery, macrophage, CD11b Dim, Crohn Cell type: Macrophage; Cd11b population: Dim; Diagnosis: Crohn's disease	Case marker detected.
Crohn's disease	Case	GSM4456475	CD3_High	Mesentery, macrophage, CD11b High, Crohn Cell type: Macrophage; Cd11b population: High; Diagnosis: Crohn's disease	Case marker detected.
Ulcerative colitis	Case	GSM4456476	NonCD3_Dim	Mesentery, macrophage, CD11b Dim, Ulcerative colitis Cell type: Macrophage; Cd11b population: Dim; Diagnosis: Ulcerative colitis	Case marker detected.
Ulcerative colitis	Case	GSM4456477	NonCD3_High	Mesentery, macrophage, CD11b High, Ulcerative colitis Cell type: Macrophage; Cd11b population: High; Diagnosis: Ulcerative colitis	Case marker detected.
Crohn's disease	Case	GSM4456478	CD4_Dim	Mesentery, macrophage, CD11b Dim, Crohn Cell type: Macrophage; Cd11b population: Dim; Diagnosis: Crohn's disease	Case marker detected.
Crohn's disease	Case	GSM4456479	CD4_High	Mesentery, macrophage, CD11b High, Crohn Cell type: Macrophage; Cd11b population: High; Diagnosis: Crohn's disease	Case marker detected.
Crohn's disease	Case	GSM4456480	CD5_Dim	Mesentery, macrophage, CD11b Dim, Crohn Cell type: Macrophage; Cd11b population: Dim; Diagnosis: Crohn's disease	Case marker detected.
Crohn's disease	Case	GSM4456481	CD5_High	Mesentery, macrophage, CD11b High, Crohn Cell type: Macrophage; Cd11b population: High; Diagnosis: Crohn's disease	Case marker detected.
Ulcerative colitis	Case	GSM4456484	NonCD5_Dim	Mesentery, macrophage, CD11b Dim, Ulcerative colitis Cell type: Macrophage; Cd11b population: Dim; Diagnosis: Ulcerative colitis	Case marker detected.
Ulcerative colitis	Case	GSM4456485	NonCD5_High	Mesentery, macrophage, CD11b High, Ulcerative colitis Cell type: Macrophage; Cd11b population: High; Diagnosis: Ulcerative colitis	Case marker detected.
Unassigned	Unassigned	GSM4456471	NonCD2_Dim	Mesentery, macrophage, CD11b Dim, IBDU Cell type: Macrophage; Cd11b population: Dim; Diagnosis: IBDU	No explicit case or control marker detected.
Unassigned	Unassigned	GSM4456472	NonCD2_High	Mesentery, macrophage, CD11b High, IBDU Cell type: Macrophage; Cd11b population: High; Diagnosis: IBDU	No explicit case or control marker detected.
Unassigned	Unassigned	GSM4456482	NonCD4_Dim	Mesentery, macrophage, CD11b Dim, NonIBD Cell type: Macrophage; Cd11b population: Dim; Diagnosis: NonIBD	No explicit case or control marker detected.
Unassigned	Unassigned	GSM4456483	NonCD4_High	Mesentery, macrophage, CD11b High, NonIBD Cell type: Macrophage; Cd11b population: High; Diagnosis: NonIBD	No explicit case or control marker detected.
Unassigned	Unassigned	GSM4456486	NonCD6_Dim	Mesentery, macrophage, CD11b Dim, NonIBD Cell type: Macrophage; Cd11b population: Dim; Diagnosis: NonIBD	No explicit case or control marker detected.
Unassigned	Unassigned	GSM4456487	NonCD6_High	Mesentery, macrophage, CD11b High, NonIBD Cell type: Macrophage; Cd11b population: High; Diagnosis: NonIBD	No explicit case or control marker detected.
Unassigned	Unassigned	GSM4456488	NonCD7_Dim	Mesentery, macrophage, CD11b Dim, NonIBD Cell type: Macrophage; Cd11b population: Dim; Diagnosis: NonIBD	No explicit case or control marker detected.
Unassigned	Unassigned	GSM4456489	NonCD7_High	Mesentery, macrophage, CD11b High, NonIBD Cell type: Macrophage; Cd11b population: High; Diagnosis: NonIBD	No explicit case or 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.