Dataset does not meet the current suitability threshold.
Whole-study downloads — these do not apply your sample requirements.
Samples meeting selected requirements: 0 cases / 0 controls
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.
Rheumatoid arthritis (RA) is a chronic, inflammatory joint disease of unknown etiology and pronounced inter-patient heterogeneity. To characterize RA at the molecular level and to uncover key pathomechanisms, we performed whole-genome gene expression analyses. Synovial tissues from rheumatoid arthritis patients were compared to those from osteoarthritis patients and to normal donors. Keywords: disease state analysis
Two disease conditions (rheumatoid arthritis and osteoarthritis) in comparison to normal donors were investigated. For the two disease groups samples derived from three individual patients and two pools of patients were hybridised.
| Source | Contribution | Status |
|---|---|---|
| GEO |
Original dataset metadata, sample metadata, source links, and GEO data availability flags.
|
Primary source |
| recount3 |
Planned trusted source for processed count availability. |
No match found |
| Expression Atlas |
Curated expression experiment linkage and source URL.
|
Available |
| PubMed |
Primary GEO citations and related PubMed articles that mention this dataset.
21 linked publications
21 DOIs
Primary publication
Related publications
|
Available |
Both case and control groups are present in the proposed grouping.
Each contrast group has at least 2 samples.
Processed data is marked available in the GEO index.
Unassigned or review-needed samples remain before analysis.
Warnings are present, but none are critical blockers.
Metadata quality is high enough to support downstream handoff.
Siftome proposed case and control labels, but no reviewer confirmation is stored yet.
Open the sample grouping CSV and confirm group labels before analysis.Both groups meet the minimum of 2 samples.
Confirm whether the cohort is large enough for the intended statistical analysis.Processed data availability is marked true in the GEO index.
Verify that downloaded processed files contain usable count or expression identifiers.0 review-needed samples and 5 unassigned samples remain.
Resolve ambiguous and unassigned samples before finalizing the contrast.No hard-excluded samples were detected by the current rules.
Record any manual exclusions in the downstream analysis notes.The dataset and sample accessions can be traced back to GEO.
Keep GEO accessions with exported metadata.Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.
Analysis readiness has blockers that must be resolved before DE.
One or more samples are unassigned and need manual grouping decisions.
Assay context may require expert handling before DESeq2-style analysis.
No active review decisions affect this ranking.
Microarray expression context was detected; compare separately from RNA-seq cohorts.
Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.
| Group | Role | Accession | Title | Source / characteristics | Reason |
|---|---|---|---|---|---|
| Rheumatoid arthritis | Case | GSM34398 | RA_A | Rheumatoid arthritis Age: 45; Gender: Female; Sample 2; Age: 81; Gender: Female | Case marker detected. |
| Rheumatoid arthritis | Case | GSM34399 | RA_B | Rheumatoid arthritis Age: 51; Gender: Male; Sample 2; Age: 84; Gender: Female; Age: 74; Gender: Female | Case marker detected. |
| Rheumatoid arthritis | Case | GSM34400 | RA_x | Rheumatoid arthritis Age: 44; Gender: Female | Case marker detected. |
| Rheumatoid arthritis | Case | GSM34401 | RA_y | Rheumatoid arthritis Age: 49; Gender: Female | Case marker detected. |
| Rheumatoid arthritis | Case | GSM34402 | RA_z | Rheumatoid arthritis Age: 63; Gender: Male | Case marker detected. |
| Normal tissue | Control | GSM34379 | ND_1 | Normal donor Age: 69; Gender: Female; Age: 64; Gender: Male; Age: 75; Gender: Male; Age: 58; Gender: Male | Control marker detected. |
| Normal tissue | Control | GSM34383 | ND_2 | Normal donor Age: 58; Gender: Male; Sample 2; Age: 58; Gender: Male; Age: 57; Gender: Male; Sample 4; Age: Unknown; Gender: Unknown | Control marker detected. |
| Normal tissue | Control | GSM34385 | ND_3 | Normal donor Age: 32; Gender: Female; Sample 2; Age: 47; Gender: Male; Sample 3; Age: 75; Gender: Female | Control marker detected. |
| Normal tissue | Control | GSM34388 | ND_4 | Normal donor Age: 46; Gender: Male; Sample 2; Age: Unknown; Gender: Unknown | Control marker detected. |
| Normal tissue | Control | GSM34391 | ND_5 | Normal donor Age: 58; Gender: Male; Sample 2; Age: Unknown; Gender: Unknown | Control marker detected. |
| Unassigned | Unassigned | GSM34393 | OA_A | Osteoarthritis Age: 60; Gender: Female; Sample 2; Age: 77; Gender: Male | No explicit case or control marker detected. |
| Unassigned | Unassigned | GSM34394 | OA_B | Osteoarthritis Age: 58; Gender: Female; Sample 2; Age: 77; Gender: Male | No explicit case or control marker detected. |
| Unassigned | Unassigned | GSM34395 | OA_x | Osteoarthritis Age: 86; Gender: Female | No explicit case or control marker detected. |
| Unassigned | Unassigned | GSM34396 | OA_y | Osteoarthritis Age: 69; Gender: Female | No explicit case or control marker detected. |
| Unassigned | Unassigned | GSM34397 | OA_z | Osteoarthritis Age: 68; Gender: Female | No explicit case or control marker detected. |
Carry Siftome's disease, organism, specimen, assay, data type, and accession into a validation project. Uncertain fields remain Unknown.