GSE111946

microRNA-218 modulates gene expression in fibroblast-like synovial cells in rheumatoid arthritis

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

2 case / 2 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
4 samples
Specimen
Tissue
Reported/interpreted study design
Disease/model vs control Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Iwamoto N
Contact name
Naoki Iwamoto
Submission date
2018-03-16
Last update
2018-09-06
Organization
Nagasaki University
Department
Immunology and Rheumatology
Public date
2018-03-26
Experiment types
Expression profiling by array
Platforms
GPL17077 Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 (Probe Name version)
Series type
Series
SubSeries
Not available
BioProject
PRJNA438659

Summary

Objective: Fibroblast-like synovial cells (FLS) have multilineage differentiation potential including osteoblasts. We aimed to investigate the role of microRNAs during the osteogenic differentiation of rheumatoid arthritis (RA)-FLS. Methods: MicroRNA(miRNA) array analysis was performed to investigate the differentially expressed miRNAs during the osteogenic differentiation. Expression of miR-218-5p (miR-218) during the osteogenic differentiation was determined by quantitative real-time PCR. Transfection with miR-218 precursor and inhibitor were used to confirm the targets of miR-218 and to analyse the ability of miR-218 to induce osteogenic differentiation. Results: The miRNA array revealed that 12 miRNAs were up-regulated and 24 miRNAs were down-regulated after osteogenic differentiation. We observed that miR-218 rose in the early phase of osteogenic differentiation and then decreased. Micro array analysis revealed the mir-218 modulate the expression of ROBO1 in RA-FLS. The induction of miR-218 in RA-FLS decreased ROBO1 expression, and promoted osteogenic differentiation.

Overall design

Number of sample:4 sample Method: For a transient transfection approach with the aim to inhibit or enhance the miR-218 function, RA-FLSs were transfected with synthetic precursor miRNA (pre-miR), with inhibitors of miR-218 (anti-miR), or with scrambled controls (Pre-miR/Anti-miR Negative Control #1; Ambion/Applied Biosystems, Foster City, CA) at a final concentration of 100 nM with the use of Lipofectamine 2000 reagent (Invitrogen, Carlsbad, CA, USA). After transfection we extracted RNA using mirVana miRNA Isolation kit(Ambion/Applied Biosystems). We investigated the gene expression after transfection of pre/anti-miR-218 using microarray.

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
4 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

  1. Osteogenic differentiation of fibroblast-like synovial cells in rheumatoid arthritis is induced by microRNA-218 through a ROBO/Slit pathway. Arthritis research & therapy, 2018
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.

Small cohort warning is present.

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 2 samples
  • Likely control group Genetic control 2 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 1 publication; 1 DOI available: PMID 30157923.
  • Publication context: Osteogenic differentiation of fibroblast-like synovial cells in rheumatoid arthritis is induced by microRNA-218 through a ROBO/Slit pathway.. Arthritis research & therapy, 2018. PMID 30157923. DOI 10.1186/s13075-018-1703-z.

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.
  • Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because fewer than six samples are too small for top-ranked 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

17 fields

Sample Group Preview

4 rows shown Show Hide
Study totals: Case 2 | Control 2 | Unassigned 0 | Excluded 0 | Ambiguous 0 4 rows shown
Group Role Accession Title Source / characteristics Reason
Rheumatoid arthritis Case GSM3045559 RASC0509 48h pre-218 Fibroblast-like synovial cells from rheumatoid arthritis Cell type: Fibroblast cells; Disease state: Rheumatoid arthritis; Condition: Synthetic precursor miR-218 Case marker detected.
Rheumatoid arthritis Case GSM3045561 RASC0509 48h anti-218 Fibroblast-like synovial cells from rheumatoid arthritis Cell type: Fibroblast cells; Disease state: Rheumatoid arthritis; Condition: Inhibitors of miR-218 Case marker detected.
Genetic control Control GSM3045558 RASC0509 48h pre-ctr Fibroblast-like synovial cells from rheumatoid arthritis Cell type: Fibroblast cells; Disease state: Rheumatoid arthritis; Condition: Scrambled control Genetic perturbation control marker detected.
Genetic control Control GSM3045560 RASC0509 48h anti-ctr Fibroblast-like synovial cells from rheumatoid arthritis Cell type: Fibroblast cells; Disease state: Rheumatoid arthritis; Condition: Anti-miR Negative Control Genetic perturbation 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.