GSE169082

Transcriptome Analysis of PBMCs in peripheral blood of patients with RA

Whole-study status Exploratory only

Dataset can inform exploration but is not strong enough for primary analysis.

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: bulk RNA-seq
Organism: Homo sapiens
Whole-study samples: 7 samples
Specimen: Biofluid
Reported/interpreted study design: Patient biofluid vs healthy control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Zhang M, Jiang Z
Contact name: zhuyan jiang
Submission date: 2021-03-17
Last update: 2021-07-14
Organization: Army Medical University
Department: Not available
Public date: 2021-07-14
Experiment types: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL20795 HiSeq X Ten (Homo sapiens)
Series type: Series
SubSeries: Not available
BioProject: PRJNA715176

Summary

The aim of this study was to analyze the expression profile of circRNAs in PBMCs in peripheral blood of patients with RA by next-generation sequencing, and to identify potential markers for early diagnosis and prognosis of RA, and to lay a foundation for further study on the mechanism of this molecule in PBMCs.

Overall design

RNA-seq of PBMCs of RA patients and normal controls. Control samples re-used from GSE120663

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 7 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. 3 linked publications 3 DOIs Primary publication circPTPN22 as a novel biomarker and ceRNA in peripheral blood mononuclear cells of rheumatoid arthritis. Molecular medicine reports, 2021 PubMed DOI Related publications Integrative analysis of lncRNAs in rheumatoid arthritis: from bioinformatics to experimental validation. Clinical and experimental medicine, 2025 PubMed DOI Molecular profiling of rheumatoid Arthritis: Expression dynamics of hsa_circ_0092125 and G6PD in an integrative gene expression study. Biochemistry and biophysics reports, 2025 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

Review before analysis

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

Secondary RNA assay context should be analyzed separately from ordinary bulk RNA-seq.

Next Steps

Review blockers and update sample grouping or dataset selection before analysis.

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.

Analysis readiness has blockers that must be resolved before DE.

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

Why This Is Ranked Here

Tumor vs normal

Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.

Applied Review Decisions

No active review decisions affect this ranking.

Derived Classifications

Disease context Rheumatoid arthritis Disease context came from Normalization rules.
Likely case group Rheumatoid arthritis 4 samples
Likely control group Healthy control 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: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 20%.
Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Rheumatoid arthritis.
Processed data is available for downstream review.
External evidence: PubMed links 3 publications; 3 DOIs available: PMID 34184082, PMID 39969652, PMID 40778323.
Publication context: circPTPN22 as a novel biomarker and ceRNA in peripheral blood mononuclear cells of rheumatoid arthritis.. Molecular medicine reports, 2021. PMID 34184082. DOI 10.3892/mmr.2021.12256.
Publication context: Integrative analysis of lncRNAs in rheumatoid arthritis: from bioinformatics to experimental validation.. Clinical and experimental medicine, 2025. PMID 39969652. DOI 10.1007/s10238-025-01589-z.
Publication context: Molecular profiling of rheumatoid Arthritis: Expression dynamics of hsa_circ_0092125 and G6PD in an integrative gene expression study.. Biochemistry and biophysics reports, 2025. PMID 40778323. DOI 10.1016/j.bbrep.2025.102180.

Cautions

Downgraded for tissue search because it is a biofluid cohort.
Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
Overall score capped because comparison suitability is weak for the selected search intent.
Overall score capped because fewer than ten samples limit cohort confidence.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.

Normalized Fields

41 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source blood GSM5176189 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood tissue: Peripheral blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5176190 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood tissue: Peripheral blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5176191 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood tissue: Peripheral blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5176192 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood tissue: Peripheral blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5176193 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood tissue: Peripheral blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5176194 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood tissue: Peripheral blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5176195 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood tissue: Peripheral blood sample-anatomical-source-v1 sample-local anatomical source

assay_type bulk RNA-seq GSE169082 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence bulk rna-seq dataset_accession: GSE169082 dataset_title: Transcriptome Analysis of PBMCs in peripheral blood of patients with RA organism: Homo sapiens assay_type: bulk RNA-seq processed_dat... keyword match keyword match: bulk rna-seq

cell_population peripheral blood mononuclear cells GSM5176189 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs RA-1 PBMCs diagnosis: RA patient; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary cell population match: pbmcs

cell_population peripheral blood mononuclear cells GSM5176190 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs RA-2 PBMCs diagnosis: RA patient; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary cell population match: pbmcs

cell_population peripheral blood mononuclear cells GSM5176191 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs RA-3 PBMCs diagnosis: RA patient; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary cell population match: pbmcs

cell_population peripheral blood mononuclear cells GSM5176192 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs RA-C PBMCs diagnosis: RA patient; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary cell population match: pbmcs

cell_population peripheral blood mononuclear cells GSM5176193 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs control_1 PBMCs diagnosis: normal control; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary cell population match: pbmcs

cell_population peripheral blood mononuclear cells GSM5176194 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs control_2 PBMCs diagnosis: normal control; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary cell population match: pbmcs

cell_population peripheral blood mononuclear cells GSM5176195 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs control_3 PBMCs diagnosis: normal control; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary cell population match: pbmcs

control_type healthy control GSM5176193 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence normal control control_1 PBMCs diagnosis: normal control; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary control type match: normal control

control_type healthy control GSM5176194 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence normal control control_2 PBMCs diagnosis: normal control; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary control type match: normal control

control_type healthy control GSM5176195 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence normal control control_3 PBMCs diagnosis: normal control; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary control type match: normal control

disease rheumatoid arthritis GSM5176189 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ra RA-1 PBMCs diagnosis: RA patient; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary disease match: ra

disease rheumatoid arthritis GSM5176190 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ra RA-2 PBMCs diagnosis: RA patient; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary disease match: ra

disease rheumatoid arthritis GSM5176191 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ra RA-3 PBMCs diagnosis: RA patient; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary disease match: ra

disease rheumatoid arthritis GSM5176192 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ra RA-C PBMCs diagnosis: RA patient; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary disease match: ra

organism Homo sapiens GSE169082 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE169082 dataset_title: Transcriptome Analysis of PBMCs in peripheral blood of patients with RA organism: Homo sapiens assay_type: bulk RNA-seq processed_dat... keyword match keyword match: homo sapiens

sample_type normal tissue GSM5176193 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal control_1 PBMCs diagnosis: normal control; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM5176194 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal control_2 PBMCs diagnosis: normal control; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM5176195 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal control_3 PBMCs diagnosis: normal control; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary sample type match: normal

specimen_material PBMC preparation GSM5176189 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs RA-1 PBMCs diagnosis: RA patient; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary specimen material match: pbmcs

specimen_material PBMC preparation GSM5176190 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs RA-2 PBMCs diagnosis: RA patient; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary specimen material match: pbmcs

specimen_material PBMC preparation GSM5176191 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs RA-3 PBMCs diagnosis: RA patient; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary specimen material match: pbmcs

specimen_material PBMC preparation GSM5176192 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs RA-C PBMCs diagnosis: RA patient; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary specimen material match: pbmcs

specimen_material PBMC preparation GSM5176193 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs control_1 PBMCs diagnosis: normal control; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary specimen material match: pbmcs

specimen_material PBMC preparation GSM5176194 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs control_2 PBMCs diagnosis: normal control; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary specimen material match: pbmcs

specimen_material PBMC preparation GSM5176195 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs control_3 PBMCs diagnosis: normal control; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary specimen material match: pbmcs

tissue blood GSE169082 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood dataset_accession: GSE169082 dataset_title: Transcriptome Analysis of PBMCs in peripheral blood of patients with RA organism: Homo sapiens assay_type: bulk RNA-seq processed_dat... controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM5176189 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood RA-1 PBMCs diagnosis: RA patient; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM5176190 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood RA-2 PBMCs diagnosis: RA patient; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM5176191 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood RA-3 PBMCs diagnosis: RA patient; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM5176192 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood RA-C PBMCs diagnosis: RA patient; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM5176193 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood control_1 PBMCs diagnosis: normal control; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM5176194 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood control_2 PBMCs diagnosis: normal control; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM5176195 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood control_3 PBMCs diagnosis: normal control; tissue: Peripheral blood; cell type: PBMCs controlled vocabulary controlled vocabulary tissue match: blood

Sample Group Preview

7 rows shown Show Hide

Study totals: Case 4 | Control 3 | Unassigned 0 | Excluded 0 | Ambiguous 0 7 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Rheumatoid arthritis	Case	GSM5176189	RA-1	PBMCs Diagnosis: RA patient; Tissue: Peripheral blood; Cell type: PBMCs	Case marker detected.
Rheumatoid arthritis	Case	GSM5176190	RA-2	PBMCs Diagnosis: RA patient; Tissue: Peripheral blood; Cell type: PBMCs	Case marker detected.
Rheumatoid arthritis	Case	GSM5176191	RA-3	PBMCs Diagnosis: RA patient; Tissue: Peripheral blood; Cell type: PBMCs	Case marker detected.
Rheumatoid arthritis	Case	GSM5176192	RA-C	PBMCs Diagnosis: RA patient; Tissue: Peripheral blood; Cell type: PBMCs	Case marker detected.
Healthy control	Control	GSM5176193	Control_1	PBMCs Diagnosis: Normal control; Tissue: Peripheral blood; Cell type: PBMCs	Sample-local control marker detected.
Healthy control	Control	GSM5176194	Control_2	PBMCs Diagnosis: Normal control; Tissue: Peripheral blood; Cell type: PBMCs	Sample-local control marker detected.
Healthy control	Control	GSM5176195	Control_3	PBMCs Diagnosis: Normal control; Tissue: Peripheral blood; Cell type: PBMCs	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

Related publications

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