GEO DataSets

(Submitter supplied) Stratifying patients on the basis of molecular signatures could facilitate development of therapeutics that target pathways specific to a particular disease or tissue location. Previous studies suggest that pathogenesis of rheumatoid arthritis (RA) is similar in all affected joints. Here we show that distinct DNA methylation and transcriptome signatures not only discriminate RA fibroblast-like synoviocytes (FLS) from osteoarthritis FLS, but also distinguish RA FLS isolated from knees and hips. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL16304

24 Samples

Download data: TXT

(Submitter supplied) Stratifying patients on the basis of molecular signatures could facilitate development of therapeutics that target pathways specific to a particular disease or tissue location. Previous studies suggest that pathogenesis of rheumatoid arthritis (RA) is similar in all affected joints. Here we show that distinct DNA methylation and transcriptome signatures not only discriminate RA fibroblast-like synoviocytes (FLS) from osteoarthritis FLS, but also distinguish RA FLS isolated from knees and hips. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

9 Samples

Download data: TXT

(Submitter supplied) Rheumatoid arthritis (RA) fibroblast‐like synoviocytes (FLS) derived from hip and knee have distinctive DNA methylation and transcriptome patterns in interleukin (IL)‐6 signaling and Janus kinase (JAK)–signal transducers and activators of transcription (STAT) pathways. To determine the functional effects of these joint‐specific signatures, we evaluated how RA hip and knee FLS differ in their response to IL‐6.Hip or knee RA FLS were obtained after arthroplasty. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

20 Samples

Download data: TXT

(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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

213 Samples

Download data: BED, BROADPEAK, NARROWPEAK, TSV

(Submitter supplied) Epigenetics is important in the pathogenesis of immune-mediated diseases like rheumatoid arthritis (RA). Here we show the first complete epigenomic characterization of RA fibroblast-like synoviocytes (FLS) by profiling histone modifications (H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3, H3K9me3), open chromatin, RNA expression and whole genome DNA methylation. To address the complex multidimensional relationship and reveal the epigenetic regulation of RA, we perform integrative analyses using a novel unbiased method to identify genomic regions with similar profiles. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

19 Samples

Download data: TSV

(Submitter supplied) Epigenetics is important in the pathogenesis of immune-mediated diseases like rheumatoid arthritis (RA). Here we show the first complete epigenomic characterization of RA fibroblast-like synoviocytes (FLS) by profiling histone modifications (H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3, H3K9me3), open chromatin, RNA expression and whole genome DNA methylation. To address the complex multidimensional relationship and reveal the epigenetic regulation of RA, we perform integrative analyses using a novel unbiased method to identify genomic regions with similar profiles. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

20 Samples

Download data: TXT

(Submitter supplied) Epigenetics is important in the pathogenesis of immune-mediated diseases like rheumatoid arthritis (RA). Here we show the first complete epigenomic characterization of RA fibroblast-like synoviocytes (FLS) by profiling histone modifications (H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3, H3K9me3), open chromatin, RNA expression and whole genome DNA methylation. To address the complex multidimensional relationship and reveal the epigenetic regulation of RA, we perform integrative analyses using a novel unbiased method to identify genomic regions with similar profiles. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

152 Samples

Download data: BROADPEAK, NARROWPEAK

(Submitter supplied) Epigenetics is important in the pathogenesis of immune-mediated diseases like rheumatoid arthritis (RA). Here we show the first complete epigenomic characterization of RA fibroblast-like synoviocytes (FLS) by profiling histone modifications (H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3, H3K9me3), open chromatin, RNA expression and whole genome DNA methylation. To address the complex multidimensional relationship and reveal the epigenetic regulation of RA, we perform integrative analyses using a novel unbiased method to identify genomic regions with similar profiles. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

22 Samples

Download data: BED

(Submitter supplied) Transcriptional profiling of mouse chondrocytes comparing chondrocytes infected with empty adenovirus and Epas1 adenovirus. RNA was extracted from each chondrocytes. We used microarrays to determine the effect of Epas1 overexpression on chondrocytes and identify the noble regulatory molecules during osteoarthritic pathogenesis.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

4 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of mouse fibroblast-like synoviocytes (FLS) comparing FLS infected with empty adenovirus and Epas1 adenovirus. RNA was extracted from each FLS. We used microarrays to determine the effect of Epas1 overexpression on FLS and identifying the noble regulatory molecules during rheumatoid arthritic pathogenesis

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

6 Samples

Download data: CEL

(Submitter supplied) We measured 371 genome‐wide DNA methylation profiles of sorted peripheral blood samples from 63 patients with rheumatoid arthritis and 31 unaffected control subjects. Methylation profiles were measured for cell subsets of CD14+ monocytes, CD19+ B cells, CD4+ memory T cells, and CD4+ naive T cells.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL16304

371 Samples

Download data: IDAT, TXT

(Submitter supplied) Discrimination of rheumatoid arthritis (RA) patients from patients with other inflammatory/degenerative joint diseases or healthy individuals purely on the basis of genes differentially expressed in high-throughput data has proven very difficult. Thus, the present study sought to achieve such discrimination by employing a novel unbiased approach using rule-based classifiers. Three multi-center genome-wide transcriptomic data sets (Affymetrix HG- U133 A/B) from a total of 79 individuals, including 20 healthy controls (control group - CG), as well as 26 osteoarthritis (OA) and 33 RA patients, were used to infer rule- based classifiers to discriminate the disease groups. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS5402

Platform:

GPL96

16 Samples

Download data: CEL

(Submitter supplied) Discrimination of rheumatoid arthritis (RA) patients from patients with other inflammatory/degenerative joint diseases or healthy individuals purely on the basis of genes differentially expressed in high-throughput data has proven very difficult. Thus, the present study sought to achieve such discrimination by employing a novel unbiased approach using rule-based classifiers. Three multi-center genome-wide transcriptomic data sets (Affymetrix HG- U133 A/B) from a total of 79 individuals, including 20 healthy controls (control group - CG), as well as 26 osteoarthritis (OA) and 33 RA patients, were used to infer rule- based classifiers to discriminate the disease groups. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS5403

Platform:

GPL96

33 Samples

Download data: CEL

(Submitter supplied) Discrimination of rheumatoid arthritis (RA) patients from patients with other inflammatory/degenerative joint diseases or healthy individuals purely on the basis of genes differentially expressed in high-throughput data has proven very difficult. Thus, the present study sought to achieve such discrimination by employing a novel unbiased approach using rule-based classifiers. Three multi-center genome-wide transcriptomic data sets (Affymetrix HG- U133 A/B) from a total of 79 individuals, including 20 healthy controls (control group - CG), as well as 26 osteoarthritis (OA) and 33 RA patients, were used to infer rule- based classifiers to discriminate the disease groups. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS5401

Platform:

GPL96

30 Samples

Download data: CEL

Analysis of synovial tissues from patients with rheumatoid arthritis or osteoarthritis. Results used to generate rule-based classifiers to distinguish patients with rheumatoid arthritis from those with osteoarthritis.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 3 disease state sets

Platform:

GPL96

Series:

GSE55457

33 Samples

Download data: CEL

Analysis of synovial tissues from patients with rheumatoid arthritis or osteoarthritis. Results used to generate rule-based classifiers to distinguish patients with rheumatoid arthritis from those with osteoarthritis.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 disease state sets

Platform:

GPL96

Series:

GSE55584

16 Samples

Download data: CEL

Analysis of synovial tissues from patients with rheumatoid arthritis or osteoarthritis. Results used to generate rule-based classifiers to distinguish patients with rheumatoid arthritis from those with osteoarthritis.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 3 disease state sets

Platform:

GPL96

Series:

GSE55235

30 Samples

Download data: CEL

(Submitter supplied) At a given time, rheumatoid arthritis (RA) is a heterogeneous disease and its underlying molecular mechanisms is still poorly understood. Because previous microarrays studies have only focused on late RA stages, we aimed to compare the biological and molecular profiles in early and long-standing (LS) RA. Synovial biopsies obtained by arthroscopy were performed in 4 early untreated RA patients, 4 LS treated RA patients and 7 control patients. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5215

45 Samples

Download data: TXT