GSE181614

RNA Sequencing facilitates quantitative analysis of lncRNA and mRNA expression in fibroblast-like synoviocytes from rheumatoid arthritis patients and trauma patients [microarray]

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

5 case / 5 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
10 samples
Specimen
Tissue
Reported/interpreted study design
Disease/model vs control Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Wang J, Shen C, Li R
Contact name
Jingnan Wang
Submission date
2021-08-07
Last update
2021-08-12
Organization
Department of Rheumatology and Immunology, The First Affiliated Hospital, Sun Yat-sen University
Department
Not available
Public date
2021-08-10
Experiment types
Expression profiling by array; Non-coding RNA profiling by array
Platforms
GPL16956 Agilent-045997 Arraystar human lncRNA microarray V3 (Probe Name Version)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA752717

Summary

Fibroblast-like synoviocytes (FLS), the active resident cell component in synovial intimal lining, play a critical role in aggressive action of synovial pannus tissue. The underlying mechanism of FLSs in the progression of RA is still unknown. To evaluate the expression pattern of lncRNA and mRNA, we preformed microarray to determine its expression profiles in FLS separated from RA patients and trauma patients.

Overall design

FLSs were seperated from synovial tissues and cutured until passage 4. Total RNA was prepared using TRIzol from HC FLS (n=5) and RA FLS (n=5) and quantified by NanoDrop ND-1000.

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
10 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.

2 linked publications 2 DOIs

Related publications

  1. Identification of serum exosomal lncRNAs and their potential regulation of characteristic genes of fibroblast-like synoviocytes in rheumatoid arthritis. International immunopharmacology, 2024
  2. LncRNA RNA XIST binding to GATA1 contributes to rheumatoid arthritis through its effects on proliferation of synovial fibroblasts and angiogenesis via regulation of CCN6. Molecular immunology, 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

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
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 Control 5 samples

Intent Interpretation

  • Downgrade or exclusion reason Downgraded assay: microarray cohorts are separated from the RNA-seq intent. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

  • Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%.
  • Interpreted disease metadata: Rheumatoid arthritis.
  • Processed data is available for downstream review.
  • External evidence: PubMed links 2 publications; 2 DOIs available: PMID 36542956, PMID 39433011.
  • Publication context: LncRNA RNA XIST binding to GATA1 contributes to rheumatoid arthritis through its effects on proliferation of synovial fibroblasts and angiogenesis via regulation of CCN6.. Molecular immunology, 2023. PMID 36542956. DOI 10.1016/j.molimm.2022.12.004.
  • Publication context: Identification of serum exosomal lncRNAs and their potential regulation of characteristic genes of fibroblast-like synoviocytes in rheumatoid arthritis.. International immunopharmacology, 2024. PMID 39433011. DOI 10.1016/j.intimp.2024.113382.

Cautions

  • Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
  • Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
  • 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

Normalized Fields

29 fields

Sample Group Preview

10 rows shown Show Hide
Study totals: Case 5 | Control 5 | Unassigned 0 | Excluded 0 | Ambiguous 0 10 rows shown
Group Role Accession Title Source / characteristics Reason
Rheumatoid arthritis Case GSM5508162 FLSs, RA patient 1 R11 Fibroblast-like synoviocytes Tissue: Synovial tissues; Cell type: Fibroblast-like synoviocytes; Disease state: Rheumatoid arthritis Case marker detected.
Rheumatoid arthritis Case GSM5508163 FLSs, RA patient 2 R20 Fibroblast-like synoviocytes Tissue: Synovial tissues; Cell type: Fibroblast-like synoviocytes; Disease state: Rheumatoid arthritis Case marker detected.
Rheumatoid arthritis Case GSM5508164 FLSs, RA patient 3 R21 Fibroblast-like synoviocytes Tissue: Synovial tissues; Cell type: Fibroblast-like synoviocytes; Disease state: Rheumatoid arthritis Case marker detected.
Rheumatoid arthritis Case GSM5508165 FLSs, RA patient 4 R8 Fibroblast-like synoviocytes Tissue: Synovial tissues; Cell type: Fibroblast-like synoviocytes; Disease state: Rheumatoid arthritis Case marker detected.
Rheumatoid arthritis Case GSM5508166 FLSs, RA patient 5 R9 Fibroblast-like synoviocytes Tissue: Synovial tissues; Cell type: Fibroblast-like synoviocytes; Disease state: Rheumatoid arthritis Case marker detected.
Control Control GSM5508167 FLSs, Trauma patient 1 N10 Fibroblast-like synoviocytes Tissue: Synovial tissues; Cell type: Fibroblast-like synoviocytes; Disease state: Control Sample-local control marker detected.
Control Control GSM5508168 FLSs, Trauma patient 2 N12 Fibroblast-like synoviocytes Tissue: Synovial tissues; Cell type: Fibroblast-like synoviocytes; Disease state: Control Sample-local control marker detected.
Control Control GSM5508169 FLSs, Trauma patient 3 N14 Fibroblast-like synoviocytes Tissue: Synovial tissues; Cell type: Fibroblast-like synoviocytes; Disease state: Control Sample-local control marker detected.
Control Control GSM5508170 FLSs, Trauma patient 4 N8 Fibroblast-like synoviocytes Tissue: Synovial tissues; Cell type: Fibroblast-like synoviocytes; Disease state: Control Sample-local control marker detected.
Control Control GSM5508171 FLSs, Trauma patient 5 N9 Fibroblast-like synoviocytes Tissue: Synovial tissues; Cell type: Fibroblast-like synoviocytes; Disease state: Control 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.