GSE148395

Effect of BET Inhibitors on Rheumatoid Synovial Fibroblast Cells [RNA-seq]

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

12 case / 12 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
bulk RNA-seq
Organism
Homo sapiens
Whole-study samples
24 samples
Specimen
Unclear specimen/source
Reported/interpreted study design
Treatment vs control Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Krishna V, Nagpal S
Contact name
Vinod Krishna
Submission date
2020-04-09
Last update
2020-12-15
Organization
Janssen R&D LLC
Department
Not available
Public date
2020-11-12
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA624140

Summary

We demonstrate that JQ1 inhibits IL1B based RA Synovial Fibroblast activation and proliferation, by inhibiting key BRD2/4 superenhancer genes.

Overall design

RNASeq of FLS cells pre and post JQ1 and IL1B treatments.

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
24 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. Integration of the Transcriptome and Genome-Wide Landscape of BRD2 and BRD4 Binding Motifs Identifies Key Superenhancer Genes and Reveals the Mechanism of Bet Inhibitor Action in Rheumatoid Arthritis Synovial Fibroblasts. Journal of immunology (Baltimore, Md. : 1950), 2021
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: Treatment status metadata normalized where treatment is part of the comparison. 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

Standard analyst review

Proceed only after the analyst confirms grouping, exclusions, and source files.

By Siftome standards, no expert review was triggered.

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

  • Disease context Rheumatoid arthritis Disease context came from Normalization rules.
  • Likely case group Treated 12 samples
  • Likely control group Untreated 12 samples

Intent Interpretation

  • Downgrade or exclusion reason Comparison: Treatment vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

  • 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 1 publication; 1 DOI available: PMID 33288543.
  • Publication context: Integration of the Transcriptome and Genome-Wide Landscape of BRD2 and BRD4 Binding Motifs Identifies Key Superenhancer Genes and Reveals the Mechanism of Bet Inhibitor Action in Rheumatoid Arthritis Synovial Fibroblasts.. Journal of immunology (Baltimore, Md. : 1950), 2021. PMID 33288543. DOI 10.4049/jimmunol.2000286.

Cautions

  • Comparison: Treatment vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
  • Downgraded for tissue search because it is a treatment/control experiment.
  • Downgraded for tissue search because study design or specimen source is unclear.
  • Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons.
  • 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.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Missing or unclear metadata. Comparison - Treatment vs control. 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

Normalized Fields

40 fields

Sample Group Preview

24 rows shown Show Hide
Study totals: Case 12 | Control 12 | Unassigned 0 | Excluded 0 | Ambiguous 0 24 rows shown
Group Role Accession Title Source / characteristics Reason
Treated Case GSM4467064 ST1303_JQ1_IL1b Fibroblast like Synoviocytes Diagnosis: Healthy; Cell type: Fibroblast like Synoviocytes; Treatment: JQ1 and IL1b; Donor: ST1303 Explicit characteristic comparison arm detected.
Treated Case GSM4467065 ST1303_JQ1 Fibroblast like Synoviocytes Diagnosis: Healthy; Cell type: Fibroblast like Synoviocytes; Treatment: JQ1; Donor: ST1303 Explicit characteristic comparison arm detected.
Treated Case GSM4467068 ST1305_JQ1_IL1b Fibroblast like Synoviocytes Diagnosis: Healthy; Cell type: Fibroblast like Synoviocytes; Treatment: JQ1 and IL1b; Donor: ST1305 Explicit characteristic comparison arm detected.
Treated Case GSM4467069 ST1305_JQ1 Fibroblast like Synoviocytes Diagnosis: Healthy; Cell type: Fibroblast like Synoviocytes; Treatment: JQ1; Donor: ST1305 Explicit characteristic comparison arm detected.
Treated Case GSM4467072 ST1359_JQ1_IL1b Fibroblast like Synoviocytes Diagnosis: Rheumatoid arthritis; Cell type: Fibroblast like Synoviocytes; Treatment: JQ1 and IL1b; Donor: ST1359 Explicit characteristic comparison arm detected.
Treated Case GSM4467073 ST1359_JQ1 Fibroblast like Synoviocytes Diagnosis: Rheumatoid arthritis; Cell type: Fibroblast like Synoviocytes; Treatment: JQ1; Donor: ST1359 Explicit characteristic comparison arm detected.
Treated Case GSM4467076 ST1385_JQ1_IL1b Fibroblast like Synoviocytes Diagnosis: Healthy; Cell type: Fibroblast like Synoviocytes; Treatment: JQ1 and IL1b; Donor: ST1385 Explicit characteristic comparison arm detected.
Treated Case GSM4467077 ST1385_JQ1 Fibroblast like Synoviocytes Diagnosis: Healthy; Cell type: Fibroblast like Synoviocytes; Treatment: JQ1; Donor: ST1385 Explicit characteristic comparison arm detected.
Treated Case GSM4467080 ST1387_JQ1_IL1b Fibroblast like Synoviocytes Diagnosis: Rheumatoid arthritis; Cell type: Fibroblast like Synoviocytes; Treatment: JQ1 and IL1b; Donor: ST1387 Explicit characteristic comparison arm detected.
Treated Case GSM4467081 ST1387_JQ1 Fibroblast like Synoviocytes Diagnosis: Rheumatoid arthritis; Cell type: Fibroblast like Synoviocytes; Treatment: JQ1; Donor: ST1387 Explicit characteristic comparison arm detected.
Treated Case GSM4467084 ST1399_JQ1_IL1b Fibroblast like Synoviocytes Diagnosis: Rheumatoid arthritis; Cell type: Fibroblast like Synoviocytes; Treatment: JQ1 and IL1b; Donor: ST1399 Explicit characteristic comparison arm detected.
Treated Case GSM4467085 ST1399_JQ1 Fibroblast like Synoviocytes Diagnosis: Rheumatoid arthritis; Cell type: Fibroblast like Synoviocytes; Treatment: JQ1; Donor: ST1399 Explicit characteristic comparison arm detected.
Untreated Control GSM4467062 ST1303_DMSO_IL1b Fibroblast like Synoviocytes Diagnosis: Healthy; Cell type: Fibroblast like Synoviocytes; Treatment: DMSO and IL1b; Donor: ST1303 Treatment control marker detected.
Untreated Control GSM4467063 ST1303_DMSO Fibroblast like Synoviocytes Diagnosis: Healthy; Cell type: Fibroblast like Synoviocytes; Treatment: DMSO; Donor: ST1303 Treatment control marker detected.
Untreated Control GSM4467066 ST1305_DMSO_IL1b Fibroblast like Synoviocytes Diagnosis: Healthy; Cell type: Fibroblast like Synoviocytes; Treatment: DMSO and IL1b; Donor: ST1305 Treatment control marker detected.
Untreated Control GSM4467067 ST1305_DMSO Fibroblast like Synoviocytes Diagnosis: Healthy; Cell type: Fibroblast like Synoviocytes; Treatment: DMSO; Donor: ST1305 Treatment control marker detected.
Untreated Control GSM4467070 ST1359_DMSO_IL1b Fibroblast like Synoviocytes Diagnosis: Rheumatoid arthritis; Cell type: Fibroblast like Synoviocytes; Treatment: DMSO and IL1b; Donor: ST1359 Treatment control marker detected.
Untreated Control GSM4467071 ST1359_DMSO Fibroblast like Synoviocytes Diagnosis: Rheumatoid arthritis; Cell type: Fibroblast like Synoviocytes; Treatment: DMSO; Donor: ST1359 Treatment control marker detected.
Untreated Control GSM4467074 ST1385_DMSO_IL1b Fibroblast like Synoviocytes Diagnosis: Healthy; Cell type: Fibroblast like Synoviocytes; Treatment: DMSO and IL1b; Donor: ST1385 Treatment control marker detected.
Untreated Control GSM4467075 ST1385_DMSO Fibroblast like Synoviocytes Diagnosis: Healthy; Cell type: Fibroblast like Synoviocytes; Treatment: DMSO; Donor: ST1385 Treatment control marker detected.
Untreated Control GSM4467078 ST1387_DMSO_IL1b Fibroblast like Synoviocytes Diagnosis: Rheumatoid arthritis; Cell type: Fibroblast like Synoviocytes; Treatment: DMSO and IL1b; Donor: ST1387 Treatment control marker detected.
Untreated Control GSM4467079 ST1387_DMSO Fibroblast like Synoviocytes Diagnosis: Rheumatoid arthritis; Cell type: Fibroblast like Synoviocytes; Treatment: DMSO; Donor: ST1387 Treatment control marker detected.
Untreated Control GSM4467082 ST1399_DMSO_IL1b Fibroblast like Synoviocytes Diagnosis: Rheumatoid arthritis; Cell type: Fibroblast like Synoviocytes; Treatment: DMSO and IL1b; Donor: ST1399 Treatment control marker detected.
Untreated Control GSM4467083 ST1399_DMSO Fibroblast like Synoviocytes Diagnosis: Rheumatoid arthritis; Cell type: Fibroblast like Synoviocytes; Treatment: DMSO; Donor: ST1399 Treatment 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.