GEO DataSets

(Submitter supplied) Fibroblast-like synoviocytes (FLS) were cultured from synovial tissues from 19 RA patients. RNA was isolated using the Fast Track 2.0 kit (Invitrogen, Carlsbad, California)from the FLS cultures. Fluorescent cDNA probes were prepared from 1 ug experimental mRNA by oligo dT-primed polymerization using Superscript II reverse transcriptase in the presence of Cy5 labeled dCTP. A common reference mRNA sample (CRE) that consists of a mixture of mRNAs isolated from 11 different cell-lines, was labeled with Cy3. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

4 related Platforms

19 Samples

Download data

(Submitter supplied) Spots were selected that had an expression level higher than 1.6 the local background. The use of a common reference sample allows the comparison of the relative expression levels across the tissue samples. All genes were expressed relative to their median expression level across the arrays of the same microarray platform, allowing us to combine the data from the 2 platforms. Data from Lymphochip and Stanford Human cDNA arrays was combined per patient. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

4 related Platforms

28 Samples

Download data

(Submitter supplied) Rheumatoid arthritis (RA) is an inflammatory joint disorder that results in progressive joint damage when insufficiently treated. In order to prevent joint destruction and functional disability in RA, early diagnosis and initiation of appropriate treatment with Disease-Modifying Antirheumatic Drugs (DMARDs) is needed. However, in daily clinical practice, patients may initially display symptoms of arthritis that do not fulfil the classification criteria for a definite diagnosis of RA, or any other joint disease, a situation called “Undifferentiated Arthritis” (UA). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4195

Platform:

GPL570

25 Samples

Download data: CEL, CHP

Analysis of synovial biopsies obtained by needle arthroscopy from affected knees of patients with systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), or osteoarthritis (OA). Results provide insight into distinct molecular mechanisms underlying SLE arthritis relative to those of OA and RA.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 5 disease state, 2 gender sets

Platform:

GPL570

Series:

GSE36700

25 Samples

Download data: CEL, CHP

(Submitter supplied) Synovial tissue mRNA from 21 RA patients and 9 OA patients is hybridized against a common reference sample on lymphochips. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL3262

31 Samples

Download data

(Submitter supplied) Rheumatoid arthritis (RA) is a heterogeneous disease. We used cDNA microarray technology to subclassify RA patients and disclose disease pathways in rheumatoid synovium. Hierarchical clustering of gene expression data identified two main groups of tissues (RA-I and RA-II). A total of 121 genes were significantly higher expressed in the RA-I tissues, whereas 39 genes were overexpressed in the RA-II tissues. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

4 related Platforms

16 Samples

Download data

(Submitter supplied) The aim of this study was to compare gene expression between two pathological groups of human synovial fibroblasts (SF) from rheumatoid arthritis (RA) and osteoarthritis (OA) synovial tissues with normal SF from healthy individuals (HSF). We used microarray expression profiling in SF cultured from OA, RA and normal synovial tissues. We found larger numbers of transcripts with differential expression in OASF compared to the other groups than in RASF compared to HSF. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

31 Samples

Download data: TXT

(Submitter supplied) Inflammatory tissues are characterized by low oxigen concentrations (hypoxia). These conditions are very different from that usually present in tissue cultures where transcriptomic profiles of human fibroblasts from inflammatory tissues have been previously analysed. The aim of this study was to characterize the changes on gene expression induced by hypoxia in human synovial fibroblasts. We used microarray expression profiling in paired normoxic and hypoxic cultures of healthy and rheumatoid arthritis (RA) synovial fibroblasts (HSF and RASF). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

36 Samples

Download data: TXT

(Submitter supplied) Objectives: TNF-induced activation of fibroblast-like synoviocytes (FLS) is a critical determinant for synovial inflammation and joint destruction in rheumatoid arthritis (RA). The detrimental role of TNF-receptor 1 (TNFR1) has thoroughly been characterized. The contributions of TNFR2, however, are largely unknown. This study was performed to delineate the role of TNFR2 in human FLS activation. Methods: TNFR2 expression in synovial tissue samples was determined by immunohistochemistry. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21290

16 Samples

Download data: TSV

(Submitter supplied) Genome-wide association studies have reported more than 100 risk loci for rheumatoid arthritis, and there loci have been shown to be enriched in immune cell-specific enhancers, we add Synovial fibroblasts (FLS), the local stromal cells of joints to this analysis. We integrated ChIP-seq, Hi-C, Capture Hi-C, ATAC-seq and RNA-seq datasets from FLS , with genetic fine-mapping of RA loci. From this we identified putative casual variants, enhancers and genes for 30-60% of RA loci and demonstrated that FLS regulatory elements accounts for up to 24% of RA heritability. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL24676 GPL16791 GPL20301

142 Samples

Download data: BED, BROADPEAK, HIC, NARROWPEAK, TXT

(Submitter supplied) Autoimmune rheumatic diseases are complex disorders, whose etiopathology is attributed to a crosstalk between genetic predisposition and environmental factors. Both variants of autoimmune susceptibility genes and environment are involved in the generation of aberrant epigenetic profiles in a cell-specific manner, which ultimately result in dysregulation of expression. Furthermore, changes in miRNA expression profiles also cause gene dysregulation associated with aberrant phenotypes. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

12 Samples

Download data: TXT

(Submitter supplied) TNF-like ligand 1A (TL1A) is a member of TNF receptor superfamily and involved in the pathogenesis of autoimmune diseases including rheumatoid arthritis (RA) by inducing apoptosis via intracellular death domain or promoting inflammation through the activation of NFκB by binding to its specific receptor death receptor 3 (DR3). Meanwhile, decoy receptor 3 (DcR3) competitively binds soluble TL1A in addition to Fas-ligand (FasL) and LIGHT and inhibits the signaling of TL1A via DR3. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

8 Samples

Download data: CEL

(Submitter supplied) Objectives: Epigenetics can influence disease susceptibility and severity. While DNA methylation of individual genes has been explored in autoimmunity, no unbiased systematic analyses have been reported. Therefore, a genome-wide evaluation of DNA methylation loci in fibroblast-like synoviocytes (FLS) isolated from the site of disease in rheumatoid arthritis (RA) was performed. Methods: Genomic DNA was isolated from six RA and five osteoarthritis (OA) FLS lines and evaluated using the Illumina HumanMethylation450 chip. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL16304

11 Samples

Download data

(Submitter supplied) Fas ligand (FasL)/TNFSF6, a member of the tumor necrosis factor (TNF) superfamily, can promote apoptosis in activated primary B cells, T cells, dendritic cells, and synovial fibroblasts through Fas and is involved in the pathogenesis of autoimmune diseases including rheumatoid arthritis (RA). Meanwhile, decoy receptor 3 (DcR3) competitively binds soluble FasL in addition to TL1A and LIGHT and inhibits the signaling of FasL via Fas. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

8 Samples

Download data: CEL

(Submitter supplied) This dataset was used to determine the influence of conditioned media from Ch and how that influence affects genome-wide gene transcription in fibroblast-like synoviocytes In this dataset, we include data from untreated fibroblast-like synoviocytes and FLS cultured in chondrocyte-conditioned media, both normal FLS (C ) and JIA FLS (J).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23159

36 Samples

Download data: CEL

(Submitter supplied) In this study, we performed RNAseq on human macropahges following a tumor necrosis factor response with and without human fibroblasts, the representative stromal cell type in the synovial lining of joints that become activated during inflammatory arthritis. Our RNAseq analysis reveals a crosstalk pathway between macrophages and fibroblasts that emerges as a result of co-culture that we call the MTF polarization phenotype. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL16791

74 Samples

Download data: TXT

(Submitter supplied) Objectives. Fibroblasts in synovium include fibroblast-like synoviocytes (FLS) in the lining and Thy1+ connective-tissue fibroblasts in the sub-lining. We aimed to investigate their developmental origin and relationship with adult progenitors. Methods. To discriminate between Gdf5-lineage cells deriving from the embryonic joint interzone and other Pdgfrα-expressing fibroblasts and progenitors, adult Gdf5-Cre;Tom;Pdgfrα-H2BGFP mice were used and cartilage injury was induced to activate progenitors. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

9 Samples

Download data: MTX, TSV

(Submitter supplied) The aim of this study was to explore the role sialic acid in synovial fibroblasts using NGS-derived transcriptome analysis (RNA-seq). Methods: Synovial fibroblasts were extracted from the synovium of healthy mice and expanded ex vivo. RNA was extracted from sialidase buffer (NT) and Clostridium perfringens Neuraminidase (CP) treated synovial fibroblast. Methods: Whole Transcriptome Profiling was generated by deep sequencing, in triplicate, using Illumina NextSeq™ 500 platform. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: TXT

(Submitter supplied) The aim of this study was to explore the role of ARNO, also known as Cyth2, in synovial fibroblasts using NGS-derived transcriptome analysis (RNA-seq). Synovial fibroblasts were isolated from mouse synovium, and stimulated with IL-1beta for 12 hours in healthy cells and cells where Cyth2 expression was knocked-down by silencing RNA. Methods: Synovial fibroblasts were extracted from the synovium of healthy mice and expanded in vitro, RNA was extracted from naïve, IL-1β stimulated and IL-1β stimulated ARNO knock-down synovial fibroblast. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

9 Samples

Download data: TXT

(Submitter supplied) Individual functions of members of the bromodomain (BRD) and extra-terminal (BET) protein family underlying the anti-inflammatory effects of BET inhibitors in rheumatoid arthritis (RA) are incompletely understood. Here we aimed to analyze regulatory functions of BRD3, an under-studied member of the BET protein family, in RA synovial fibroblasts (FLS). BRD3 was silenced in FLS prior to stimulation with TNF. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: CSV