Interplay of NLRC4/NLRP3 inflammasomes and Fc-ˠ-Receptors on CD1c+ DC Associates with Pathogenic IFNˠ+IL17+ T cells and RA Severity

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

21 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: 42 samples
Specimen: Mixed specimen/source
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Delgado-Arévalo C, Calvet-Mirabent M, Triguero-Martinez A, Vázquez de Luis E, Benguría A, Calzada-Fraile D, Sánchez-Cerrillo I, Moreno-Vellisca R, de la Fuente H, Ramiro A, Sánchez-Madrid F, Castañeda S, Dopazo A, Gonzalez-Álvaro I, Martín-Gayo E, Vazquez de Luis E
Contact name: Enrique Vazquez de Luis
Submission date: 2020-08-28
Last update: 2023-12-13
Organization: Universidad de Zaragoza
Department: SAI
Public date: 2022-12-21
Experiment types: Expression profiling by high throughput sequencing
Platforms: GPL16791 Illumina HiSeq 2500 (Homo sapiens); GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Series type: Series
SubSeries: Not available
BioProject: PRJNA659983

Summary

Deregulated myeloid cells infiltrating to the joints likely contribute to rheumatoid arthritis (RA) pathogenesis through multiple mechanisms, including the secretion of proinflammatory cytokines and the induction of pathogenic adaptive Th17 cells, that mediate joint damage. However, the individual contribution of specific myeloid subsets such as CD1c+ and CD141+ conventional dendritic cells (cDC) to RA development and progression has been poorly studied and remains unclear. In particular, the potential molecular mechanisms specifically affecting CD1c+ cDCs in RA patients and their functional implications have not been characterized. Using RNA-seq, multiparametric flow cytometry and in vitro functional assays, we compared in parallel transcriptional, phenotypical and functional characteristics of monocytes, CD1c+ and CD141+ cDCs from the blood and synovial fluid of RA patients.

Overall design

We performed RNA sequencing using RNA from Monocytes, Dendritic Cd1c+ and Dendritic Cd141 cells obtained from blood/sinovial fluid of Rheumatoid Arthritis versus healthy/CPPD matched controls.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 42 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 Primary publication NLRC4-mediated activation of CD1c+ DC contributes to perpetuation of synovitis in rheumatoid arthritis. JCI insight, 2022 PubMed DOI MICa/b-dependent activation of natural killer cells by CD64(+) inflammatory type 2 dendritic cells contributes to autoimmunity. The EMBO journal, 2023 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

85% 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

3/15 pts

Unassigned or review-needed samples remain before analysis.

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

9 samples are still unassigned.

Next Steps

Resolve unassigned or review-needed samples in the grouping table.

Analysis Preparation Checklist

4/6 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

Needs review

0 review-needed samples and 9 unassigned samples remain.

Resolve ambiguous and unassigned samples before finalizing the contrast.

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.

One or more samples are unassigned and need manual grouping decisions.

Mixed specimen/source groups must be separated before 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

Disease context Rheumatoid arthritis Disease context came from Normalization rules.
Likely case group Rheumatoid arthritis 21 samples
Likely control group Control 12 samples

Intent Interpretation

Downgrade or exclusion reason Downgraded for tissue search because specimen/source classes are mixed. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

Comparison: Disease/model vs control. Specimen: Mixed specimen/source. Comparison suitability: 0%.
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 2 publications; 2 DOIs available: PMID 36194479, PMID 37916875.
Publication context: NLRC4-mediated activation of CD1c+ DC contributes to perpetuation of synovitis in rheumatoid arthritis.. JCI insight, 2022. PMID 36194479. DOI 10.1172/jci.insight.152886.
Publication context: MICa/b-dependent activation of natural killer cells by CD64(+) inflammatory type 2 dendritic cells contributes to autoimmunity.. The EMBO journal, 2023. PMID 37916875. DOI 10.15252/embj.2023113714.

Cautions

Downgraded for tissue search because specimen/source classes are mixed.
Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
Mixed specimen/source dataset downgraded until tissue samples are clearly separated.
Overall score capped because comparison suitability is weak for the selected search intent.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.

Normalized Fields

88 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source blood GSM4751504 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751505 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751506 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751507 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751508 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751509 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751510 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751511 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751512 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751513 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751514 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751515 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751516 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751517 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751518 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751519 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751520 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751521 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751522 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751523 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751524 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751525 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751526 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM4751527 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

assay_type bulk RNA-seq GSE157047 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence bulk rna-seq dataset_accession: GSE157047 dataset_title: Interplay of NLRC4/NLRP3 inflammasomes and Fc-ˠ-Receptors on CD1c+ DC Associates with Pathogenic IFNˠ+IL17+ T cells and RA Severity o... keyword match keyword match: bulk rna-seq

cell_population monocytes GSM4751506 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence monocytes Blood_Mo_ARC255 Blood tissue: Blood; cell type: Monocytes; diagnosis: Rheumatoid Arthritis; library type: Stranded controlled vocabulary controlled vocabulary cell population match: monocytes

cell_population monocytes GSM4751509 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence monocytes Blood_Mo_ARC338 Blood tissue: Blood; cell type: Monocytes; diagnosis: Rheumatoid Arthritis; library type: Stranded controlled vocabulary controlled vocabulary cell population match: monocytes

cell_population monocytes GSM4751512 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence monocytes Blood_Mo_ARC376 Blood tissue: Blood; cell type: Monocytes; diagnosis: Rheumatoid Arthritis; library type: Stranded controlled vocabulary controlled vocabulary cell population match: monocytes

cell_population monocytes GSM4751515 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence monocytes Blood_Mo_ARC382 Blood tissue: Blood; cell type: Monocytes; diagnosis: Rheumatoid Arthritis; library type: Stranded controlled vocabulary controlled vocabulary cell population match: monocytes

cell_population monocytes GSM4751518 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence monocytes Blood_Mo_BK114 Blood tissue: Blood; cell type: Monocytes; diagnosis: Control; library type: Stranded controlled vocabulary controlled vocabulary cell population match: monocytes

cell_population monocytes GSM4751521 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence monocytes Blood_Mo_BK32 Blood tissue: Blood; cell type: Monocytes; diagnosis: Control; library type: Stranded controlled vocabulary controlled vocabulary cell population match: monocytes

cell_population monocytes GSM4751526 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence monocytes Blood_Mo_BK42 Blood tissue: Blood; cell type: Monocytes; diagnosis: Control; library type: Stranded controlled vocabulary controlled vocabulary cell population match: monocytes

cell_population monocytes GSM4751527 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence monocytes Blood_Mo_BK43 Blood tissue: Blood; cell type: Monocytes; diagnosis: Control; library type: Stranded controlled vocabulary controlled vocabulary cell population match: monocytes

cell_population monocytes GSM4751537 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence monocytes Sinovial_Mo_AR_LS237 Sinovial Fluid tissue: Sinovial Fluid; cell type: Monocytes; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary cell population match: monocytes

cell_population monocytes GSM4751538 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence monocytes Sinovial_Mo_AR_LS238 Sinovial Fluid tissue: Sinovial Fluid; cell type: Monocytes; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary cell population match: monocytes

cell_population monocytes GSM4751539 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence monocytes Sinovial_Mo_AR_LS241 Sinovial Fluid tissue: Sinovial Fluid; cell type: Monocytes; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary cell population match: monocytes

cell_population monocytes GSM4751540 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence monocytes Sinovial_Mo_Condro_LS247 Sinovial Fluid tissue: Sinovial Fluid; cell type: Monocytes; diagnosis: CPPD; library type: Low Input controlled vocabulary controlled vocabulary cell population match: monocytes

cell_population monocytes GSM4751541 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence monocytes Sinovial_Mo_Condro_LS248 Sinovial Fluid tissue: Sinovial Fluid; cell type: Monocytes; diagnosis: CPPD; library type: Low Input controlled vocabulary controlled vocabulary cell population match: monocytes

cell_population monocytes GSM4751542 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence monocytes Sinovial_Mo_Condro_LS225 Sinovial Fluid tissue: Sinovial Fluid; cell type: Monocytes; diagnosis: CPPD; library type: Low Input controlled vocabulary controlled vocabulary cell population match: monocytes

disease rheumatoid arthritis GSE157047 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis dataset_accession: GSE157047 dataset_title: Interplay of NLRC4/NLRP3 inflammasomes and Fc-ˠ-Receptors on CD1c+ DC Associates with Pathogenic IFNˠ+IL17+ T cells and RA Severity o... controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4751504 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Blood_Cd141_ARC255 Blood tissue: Blood; cell type: Dendritic Cells Cd141+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4751505 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Blood_Cd1c_ARC255 Blood tissue: Blood; cell type: Dendritic Cells Cd1c+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4751506 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Blood_Mo_ARC255 Blood tissue: Blood; cell type: Monocytes; diagnosis: Rheumatoid Arthritis; library type: Stranded controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4751507 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Blood_Cd141_ARC338 Blood tissue: Blood; cell type: Dendritic Cells Cd141+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4751508 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Blood_Cd1c_ARC338 Blood tissue: Blood; cell type: Dendritic Cells Cd1c+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4751509 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Blood_Mo_ARC338 Blood tissue: Blood; cell type: Monocytes; diagnosis: Rheumatoid Arthritis; library type: Stranded controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4751510 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Blood_Cd141_ARC376 Blood tissue: Blood; cell type: Dendritic Cells Cd141+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4751511 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Blood_Cd1c_ARC376 Blood tissue: Blood; cell type: Dendritic Cells Cd1c+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4751512 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Blood_Mo_ARC376 Blood tissue: Blood; cell type: Monocytes; diagnosis: Rheumatoid Arthritis; library type: Stranded controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4751513 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Blood_Cd141_ARC382 Blood tissue: Blood; cell type: Dendritic Cells Cd141+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4751514 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Blood_Cd1c_ARC382 Blood tissue: Blood; cell type: Dendritic Cells Cd1c+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4751515 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Blood_Mo_ARC382 Blood tissue: Blood; cell type: Monocytes; diagnosis: Rheumatoid Arthritis; library type: Stranded controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4751531 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Sinovial_Cd141_AR_LS237 Sinovial Fluid tissue: Sinovial Fluid; cell type: Dendritic Cells Cd141+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4751532 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Sinovial_Cd141_AR_LS238 Sinovial Fluid tissue: Sinovial Fluid; cell type: Dendritic Cells Cd141+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4751533 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Sinovial_Cd141_AR_LS241 Sinovial Fluid tissue: Sinovial Fluid; cell type: Dendritic Cells Cd141+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4751537 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Sinovial_Mo_AR_LS237 Sinovial Fluid tissue: Sinovial Fluid; cell type: Monocytes; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4751538 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Sinovial_Mo_AR_LS238 Sinovial Fluid tissue: Sinovial Fluid; cell type: Monocytes; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4751539 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Sinovial_Mo_AR_LS241 Sinovial Fluid tissue: Sinovial Fluid; cell type: Monocytes; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4751543 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Sinovial_Cd1c_AR_LS237 Sinovial Fluid tissue: Sinovial Fluid; cell type: Dendritic Cells Cd1c+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4751544 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Sinovial_Cd1c_AR_LS238 Sinovial Fluid tissue: Sinovial Fluid; cell type: Dendritic Cells Cd1c+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4751545 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Sinovial_Cd1c_AR_LS241 Sinovial Fluid tissue: Sinovial Fluid; cell type: Dendritic Cells Cd1c+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

organism Homo sapiens GSE157047 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE157047 dataset_title: Interplay of NLRC4/NLRP3 inflammasomes and Fc-ˠ-Receptors on CD1c+ DC Associates with Pathogenic IFNˠ+IL17+ T cells and RA Severity o... keyword match keyword match: homo sapiens

tissue blood GSE157047 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood dataset_accession: GSE157047 dataset_title: Interplay of NLRC4/NLRP3 inflammasomes and Fc-ˠ-Receptors on CD1c+ DC Associates with Pathogenic IFNˠ+IL17+ T cells and RA Severity o... controlled vocabulary controlled vocabulary tissue match: blood

tissue synovium GSE157047 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence synovial dataset_accession: GSE157047 dataset_title: Interplay of NLRC4/NLRP3 inflammasomes and Fc-ˠ-Receptors on CD1c+ DC Associates with Pathogenic IFNˠ+IL17+ T cells and RA Severity o... controlled vocabulary controlled vocabulary tissue match: synovial

tissue blood GSM4751504 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Cd141_ARC255 Blood tissue: Blood; cell type: Dendritic Cells Cd141+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751505 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Cd1c_ARC255 Blood tissue: Blood; cell type: Dendritic Cells Cd1c+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751506 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Mo_ARC255 Blood tissue: Blood; cell type: Monocytes; diagnosis: Rheumatoid Arthritis; library type: Stranded controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751507 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Cd141_ARC338 Blood tissue: Blood; cell type: Dendritic Cells Cd141+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751508 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Cd1c_ARC338 Blood tissue: Blood; cell type: Dendritic Cells Cd1c+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751509 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Mo_ARC338 Blood tissue: Blood; cell type: Monocytes; diagnosis: Rheumatoid Arthritis; library type: Stranded controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751510 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Cd141_ARC376 Blood tissue: Blood; cell type: Dendritic Cells Cd141+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751511 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Cd1c_ARC376 Blood tissue: Blood; cell type: Dendritic Cells Cd1c+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751512 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Mo_ARC376 Blood tissue: Blood; cell type: Monocytes; diagnosis: Rheumatoid Arthritis; library type: Stranded controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751513 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Cd141_ARC382 Blood tissue: Blood; cell type: Dendritic Cells Cd141+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751514 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Cd1c_ARC382 Blood tissue: Blood; cell type: Dendritic Cells Cd1c+; diagnosis: Rheumatoid Arthritis; library type: Low Input controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751515 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Mo_ARC382 Blood tissue: Blood; cell type: Monocytes; diagnosis: Rheumatoid Arthritis; library type: Stranded controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751516 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Cd141_BK114 Blood tissue: Blood; cell type: Dendritic Cells Cd141+; diagnosis: Control; library type: Low Input controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751517 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Cd1c_BK114 Blood tissue: Blood; cell type: Dendritic Cells Cd1c+; diagnosis: Control; library type: Low Input controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751518 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Mo_BK114 Blood tissue: Blood; cell type: Monocytes; diagnosis: Control; library type: Stranded controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751519 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Cd141_BK32 Blood tissue: Blood; cell type: Dendritic Cells Cd141+; diagnosis: Control; library type: Low Input controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751520 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Cd1c_BK32 Blood tissue: Blood; cell type: Dendritic Cells Cd1c+; diagnosis: Control; library type: Low Input controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751521 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Mo_BK32 Blood tissue: Blood; cell type: Monocytes; diagnosis: Control; library type: Stranded controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751522 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Cd141_BK42 Blood tissue: Blood; cell type: Dendritic Cells Cd141+; diagnosis: Control; library type: Low Input controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751523 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Cd1c_BK42 Blood tissue: Blood; cell type: Dendritic Cells Cd1c+; diagnosis: Control; library type: Low Input controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751524 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Cd141_BK43 Blood tissue: Blood; cell type: Dendritic Cells Cd141+; diagnosis: Control; library type: Low Input controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751525 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Cd1c_BK43 Blood tissue: Blood; cell type: Dendritic Cells Cd1c+; diagnosis: Control; library type: Low Input controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751526 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Mo_BK42 Blood tissue: Blood; cell type: Monocytes; diagnosis: Control; library type: Stranded controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM4751527 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Blood_Mo_BK43 Blood tissue: Blood; cell type: Monocytes; diagnosis: Control; library type: Stranded controlled vocabulary controlled vocabulary tissue match: blood

Sample Group Preview

42 rows shown Show Hide

Study totals: Case 21 | Control 12 | Unassigned 9 | Excluded 0 | Ambiguous 0 42 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Rheumatoid arthritis	Case	GSM4751504	Blood_Cd141_ARC255	Blood Tissue: Blood; Cell type: Dendritic Cells Cd141+; Diagnosis: Rheumatoid Arthritis; Library type: Low Input	Case marker detected.
Rheumatoid arthritis	Case	GSM4751505	Blood_Cd1c_ARC255	Blood Tissue: Blood; Cell type: Dendritic Cells Cd1c+; Diagnosis: Rheumatoid Arthritis; Library type: Low Input	Case marker detected.
Rheumatoid arthritis	Case	GSM4751506	Blood_Mo_ARC255	Blood Tissue: Blood; Cell type: Monocytes; Diagnosis: Rheumatoid Arthritis; Library type: Stranded	Case marker detected.
Rheumatoid arthritis	Case	GSM4751507	Blood_Cd141_ARC338	Blood Tissue: Blood; Cell type: Dendritic Cells Cd141+; Diagnosis: Rheumatoid Arthritis; Library type: Low Input	Case marker detected.
Rheumatoid arthritis	Case	GSM4751508	Blood_Cd1c_ARC338	Blood Tissue: Blood; Cell type: Dendritic Cells Cd1c+; Diagnosis: Rheumatoid Arthritis; Library type: Low Input	Case marker detected.
Rheumatoid arthritis	Case	GSM4751509	Blood_Mo_ARC338	Blood Tissue: Blood; Cell type: Monocytes; Diagnosis: Rheumatoid Arthritis; Library type: Stranded	Case marker detected.
Rheumatoid arthritis	Case	GSM4751510	Blood_Cd141_ARC376	Blood Tissue: Blood; Cell type: Dendritic Cells Cd141+; Diagnosis: Rheumatoid Arthritis; Library type: Low Input	Case marker detected.
Rheumatoid arthritis	Case	GSM4751511	Blood_Cd1c_ARC376	Blood Tissue: Blood; Cell type: Dendritic Cells Cd1c+; Diagnosis: Rheumatoid Arthritis; Library type: Low Input	Case marker detected.
Rheumatoid arthritis	Case	GSM4751512	Blood_Mo_ARC376	Blood Tissue: Blood; Cell type: Monocytes; Diagnosis: Rheumatoid Arthritis; Library type: Stranded	Case marker detected.
Rheumatoid arthritis	Case	GSM4751513	Blood_Cd141_ARC382	Blood Tissue: Blood; Cell type: Dendritic Cells Cd141+; Diagnosis: Rheumatoid Arthritis; Library type: Low Input	Case marker detected.
Rheumatoid arthritis	Case	GSM4751514	Blood_Cd1c_ARC382	Blood Tissue: Blood; Cell type: Dendritic Cells Cd1c+; Diagnosis: Rheumatoid Arthritis; Library type: Low Input	Case marker detected.
Rheumatoid arthritis	Case	GSM4751515	Blood_Mo_ARC382	Blood Tissue: Blood; Cell type: Monocytes; Diagnosis: Rheumatoid Arthritis; Library type: Stranded	Case marker detected.
Rheumatoid arthritis	Case	GSM4751531	Sinovial_Cd141_AR_LS237	Sinovial Fluid Tissue: Sinovial Fluid; Cell type: Dendritic Cells Cd141+; Diagnosis: Rheumatoid Arthritis; Library type: Low Input	Case marker detected.
Rheumatoid arthritis	Case	GSM4751532	Sinovial_Cd141_AR_LS238	Sinovial Fluid Tissue: Sinovial Fluid; Cell type: Dendritic Cells Cd141+; Diagnosis: Rheumatoid Arthritis; Library type: Low Input	Case marker detected.
Rheumatoid arthritis	Case	GSM4751533	Sinovial_Cd141_AR_LS241	Sinovial Fluid Tissue: Sinovial Fluid; Cell type: Dendritic Cells Cd141+; Diagnosis: Rheumatoid Arthritis; Library type: Low Input	Case marker detected.
Rheumatoid arthritis	Case	GSM4751537	Sinovial_Mo_AR_LS237	Sinovial Fluid Tissue: Sinovial Fluid; Cell type: Monocytes; Diagnosis: Rheumatoid Arthritis; Library type: Low Input	Case marker detected.
Rheumatoid arthritis	Case	GSM4751538	Sinovial_Mo_AR_LS238	Sinovial Fluid Tissue: Sinovial Fluid; Cell type: Monocytes; Diagnosis: Rheumatoid Arthritis; Library type: Low Input	Case marker detected.
Rheumatoid arthritis	Case	GSM4751539	Sinovial_Mo_AR_LS241	Sinovial Fluid Tissue: Sinovial Fluid; Cell type: Monocytes; Diagnosis: Rheumatoid Arthritis; Library type: Low Input	Case marker detected.
Rheumatoid arthritis	Case	GSM4751543	Sinovial_Cd1c_AR_LS237	Sinovial Fluid Tissue: Sinovial Fluid; Cell type: Dendritic Cells Cd1c+; Diagnosis: Rheumatoid Arthritis; Library type: Low Input	Case marker detected.
Rheumatoid arthritis	Case	GSM4751544	Sinovial_Cd1c_AR_LS238	Sinovial Fluid Tissue: Sinovial Fluid; Cell type: Dendritic Cells Cd1c+; Diagnosis: Rheumatoid Arthritis; Library type: Low Input	Case marker detected.
Rheumatoid arthritis	Case	GSM4751545	Sinovial_Cd1c_AR_LS241	Sinovial Fluid Tissue: Sinovial Fluid; Cell type: Dendritic Cells Cd1c+; Diagnosis: Rheumatoid Arthritis; Library type: Low Input	Case marker detected.
Control	Control	GSM4751516	Blood_Cd141_BK114	Blood Tissue: Blood; Cell type: Dendritic Cells Cd141+; Diagnosis: Control; Library type: Low Input	Sample-local control marker detected.
Control	Control	GSM4751517	Blood_Cd1c_BK114	Blood Tissue: Blood; Cell type: Dendritic Cells Cd1c+; Diagnosis: Control; Library type: Low Input	Sample-local control marker detected.
Control	Control	GSM4751518	Blood_Mo_BK114	Blood Tissue: Blood; Cell type: Monocytes; Diagnosis: Control; Library type: Stranded	Sample-local control marker detected.
Control	Control	GSM4751519	Blood_Cd141_BK32	Blood Tissue: Blood; Cell type: Dendritic Cells Cd141+; Diagnosis: Control; Library type: Low Input	Sample-local control marker detected.
Control	Control	GSM4751520	Blood_Cd1c_BK32	Blood Tissue: Blood; Cell type: Dendritic Cells Cd1c+; Diagnosis: Control; Library type: Low Input	Sample-local control marker detected.
Control	Control	GSM4751521	Blood_Mo_BK32	Blood Tissue: Blood; Cell type: Monocytes; Diagnosis: Control; Library type: Stranded	Sample-local control marker detected.
Control	Control	GSM4751522	Blood_Cd141_BK42	Blood Tissue: Blood; Cell type: Dendritic Cells Cd141+; Diagnosis: Control; Library type: Low Input	Sample-local control marker detected.
Control	Control	GSM4751523	Blood_Cd1c_BK42	Blood Tissue: Blood; Cell type: Dendritic Cells Cd1c+; Diagnosis: Control; Library type: Low Input	Sample-local control marker detected.
Control	Control	GSM4751524	Blood_Cd141_BK43	Blood Tissue: Blood; Cell type: Dendritic Cells Cd141+; Diagnosis: Control; Library type: Low Input	Sample-local control marker detected.
Control	Control	GSM4751525	Blood_Cd1c_BK43	Blood Tissue: Blood; Cell type: Dendritic Cells Cd1c+; Diagnosis: Control; Library type: Low Input	Sample-local control marker detected.
Control	Control	GSM4751526	Blood_Mo_BK42	Blood Tissue: Blood; Cell type: Monocytes; Diagnosis: Control; Library type: Stranded	Sample-local control marker detected.
Control	Control	GSM4751527	Blood_Mo_BK43	Blood Tissue: Blood; Cell type: Monocytes; Diagnosis: Control; Library type: Stranded	Sample-local control marker detected.
Unassigned	Unassigned	GSM4751528	Sinovial_Cd1c_Condro_LS247	Sinovial Fluid Tissue: Sinovial Fluid; Cell type: Dendritic Cells Cd1c+; Diagnosis: CPPD; Library type: Low Input	No explicit case or control marker detected.
Unassigned	Unassigned	GSM4751529	Sinovial_Cd1c_Condro_LS248	Sinovial Fluid Tissue: Sinovial Fluid; Cell type: Dendritic Cells Cd1c+; Diagnosis: CPPD; Library type: Low Input	No explicit case or control marker detected.
Unassigned	Unassigned	GSM4751530	Sinovial_Cd1c_Condro_LS225	Sinovial Fluid Tissue: Sinovial Fluid; Cell type: Dendritic Cells Cd1c+; Diagnosis: CPPD; Library type: Low Input	No explicit case or control marker detected.
Unassigned	Unassigned	GSM4751534	Sinovial_Cd141_Condro_LS247	Sinovial Fluid Tissue: Sinovial Fluid; Cell type: Dendritic Cells Cd141+; Diagnosis: CPPD; Library type: Low Input	No explicit case or control marker detected.
Unassigned	Unassigned	GSM4751535	Sinovial_Cd141_Condro_LS248	Sinovial Fluid Tissue: Sinovial Fluid; Cell type: Dendritic Cells Cd141+; Diagnosis: CPPD; Library type: Low Input	No explicit case or control marker detected.
Unassigned	Unassigned	GSM4751536	Sinovial_Cd141_Condro_LS225	Sinovial Fluid Tissue: Sinovial Fluid; Cell type: Dendritic Cells Cd141+; Diagnosis: CPPD; Library type: Low Input	No explicit case or control marker detected.
Unassigned	Unassigned	GSM4751540	Sinovial_Mo_Condro_LS247	Sinovial Fluid Tissue: Sinovial Fluid; Cell type: Monocytes; Diagnosis: CPPD; Library type: Low Input	No explicit case or control marker detected.
Unassigned	Unassigned	GSM4751541	Sinovial_Mo_Condro_LS248	Sinovial Fluid Tissue: Sinovial Fluid; Cell type: Monocytes; Diagnosis: CPPD; Library type: Low Input	No explicit case or control marker detected.
Unassigned	Unassigned	GSM4751542	Sinovial_Mo_Condro_LS225	Sinovial Fluid Tissue: Sinovial Fluid; Cell type: Monocytes; Diagnosis: CPPD; Library type: Low Input	No explicit case or control marker detected.

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