GSE10500

Gene expression in rheumatoid arthritis synovial macrophages

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

0 case / 3 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
8 samples
Specimen
Biofluid
Reported/interpreted study design
Disease/model vs control Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Ivashkiv LB, Antoniv TT, Hu X, Anna Y, Park-Min K, Antoniv T
Contact name
Taras Antoniv
Submission date
2008-02-12
Last update
2018-12-13
Organization
Hospital for Special Surgery
Department
Research
Public date
2008-02-14
Experiment types
Expression profiling by array
Platforms
GPL8300 [HG_U95Av2] Affymetrix Human Genome U95 Version 2 Array
Series type
Series
SubSeries
Not available
BioProject
PRJNA107955

Summary

Macrophages from RA synovial fluids were compared to primary human blood-derived macrophages. Keywords: disease state analysis

Overall design

Macrophages from synovial fluids of five RA patients were isolated by ficoll density gradient centrifugation, followed by positive selection of CD14+ cells using magnetic beads. The patients’ diagnoses were determined by their physicians, in each case a Board-certified rheumatologist at the Hospital for Special Surgery, and were definite RA according to American College of Rheumatology criteria. De-identified samples were processed in an anonymous manner using a protocol approved by the Institutional Review Board of the Hospital for Special Surgery. Human peripheral blood mononuclear cells were isolated from venous blood of independent healthy donors by centrifugation on a Ficoll density gradient. Monocytes were obtained from PBMCs using anti-CD14 magnetic beads, and were >96% pure as verified by flow cytometry. Monocytes were differentiated into macrophages by culturing in RPMI 1640 medium supplemented with 10% fetal bovine serum and M-CSF (20 ng/ml). The viability and purity of macrophages was comparable in all conditions Gene expression was analyzed using Affymetrix microarrays and protocols.

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
8 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.

5 linked publications 4 DOIs

Primary publication

  1. TNF activates an IRF1-dependent autocrine loop leading to sustained expression of chemokines and STAT1-dependent type I interferon-response genes. Nature immunology, 2008

Related publications

  1. Identification and Experimental Verification of PDK4 as a Potential Biomarker for Diagnosis and Treatment in Rheumatoid Arthritis. Molecular biotechnology, 2025
  2. KLF11 alleviates rheumatoid arthritis by regulating M1 macrophage polarization via downregulation of YAP1 expression. Arthritis research & therapy, 2025
  3. Identification of Candidate Genes Related to Synovial Macrophages in Rheumatoid Arthritis by Bioinformatics Analysis. International journal of general medicine, 2021
  4. Dissecting the Imbalance of Synovial Macrophages in Rheumatoid Arthritis. Alternative therapies in health and medicine, 2023
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 Rheumatoid arthritis Disease context came from Normalization rules.
  • Likely case group Rheumatoid arthritis 5 samples
  • Likely control group Normal tissue 3 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: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
  • Interpreted disease metadata: Rheumatoid arthritis.
  • Processed data is available for downstream review.
  • External evidence: PubMed links 5 publications; 4 DOIs available: PMID 18345002, PMID 34764682, PMID 37573587, PMID 39466354, PMID 40859359.
  • Publication context: TNF activates an IRF1-dependent autocrine loop leading to sustained expression of chemokines and STAT1-dependent type I interferon-response genes.. Nature immunology, 2008. PMID 18345002. DOI 10.1038/ni1576.
  • Publication context: Identification of Candidate Genes Related to Synovial Macrophages in Rheumatoid Arthritis by Bioinformatics Analysis.. International journal of general medicine, 2021. PMID 34764682. DOI 10.2147/IJGM.S333512.
  • Publication context: Dissecting the Imbalance of Synovial Macrophages in Rheumatoid Arthritis.. Alternative therapies in health and medicine, 2023. PMID 37573587.
  • Publication context: 2 additional linked PubMed publications are available.

Cautions

  • Downgraded for tissue search because it is a biofluid cohort.
  • Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
  • Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
  • 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 fewer than ten samples limit cohort confidence.
  • 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

Normalized Fields

26 fields

Sample Group Preview

8 rows shown Show Hide
Study totals: Case 5 | Control 3 | Unassigned 0 | Excluded 0 | Ambiguous 0 8 rows shown
Group Role Accession Title Source / characteristics Reason
Rheumatoid arthritis Case GSM265020 Rheumatoid arthritis 9252 RA patient Synovial fluid macrophages Case marker detected.
Rheumatoid arthritis Case GSM265036 Rheumatoid arthritis 121102 RA patient Synovial fluid macrophages Case marker detected.
Rheumatoid arthritis Case GSM265361 Rheumatoid arthritis 2-21 RA patient Synovial fluid macrophages Case marker detected.
Rheumatoid arthritis Case GSM265363 Rheumatoid arthritis 1032 RA patient Synovial fluid macrophages Case marker detected.
Rheumatoid arthritis Case GSM265366 Rheumatoid arthritis 1152 RA patient Synovial fluid macrophages Case marker detected.
Normal tissue Control GSM265436 Normal donors XH1 Normal donors Blood-derived macrophages Control marker detected.
Normal tissue Control GSM265439 Normal donors XCH1 Normal donors Blood-derived macrophages Control marker detected.
Normal tissue Control GSM265445 Normal donors TA1 Normal donors Blood-derived macrophages Control marker detected.

Use as Discovery Cohort

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Carry Siftome's disease, organism, specimen, assay, data type, and accession into a validation project. Uncertain fields remain Unknown.