GEO DataSets

(Submitter supplied) The mechanisms that determine the efficacy or inefficacy of methotrexate in juvenile idiopathic arthritis (JIA) are ill-defined. The objective of this study was to identify a gene expression transcriptional signature associated with poor response to MTX in patients with JIA. RNA sequencing was used to measure gene expression in peripheral blood mononuclear cells (PBMC) collected from 47 patients with JIA prior to MTX treatment and 14 age-matched controls. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

61 Samples

Download data: TXT

(Submitter supplied) Gene expression on peripheral blood mononuclear cells (PBMC) from SPARKS CHARMS juvenile idiopathic arthritis (JIA) cohort pre and post methotrexate therapy. This is the first study to our knowledge, to evaluate gene expression profiles in children with JIA before and after MTX, and to analyze genetic variation in differentially expressed genes. We have identified a gene, which may contribute to genetic variability in MTX response in JIA.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4272

Platform:

GPL570

22 Samples

Download data: CEL

Analysis of PBMC from 11 patients with juvenile idiopathic arthritis (JIA) following 6 months of methotrexate (MTX) therapy. Individual response to MTX is variable. Results provide insight into the molecular mechanisms underlying response to MTX in JIA.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 agent, 2 disease state, 11 individual sets

Platform:

GPL570

Series:

GSE23687

22 Samples

Download data: CEL

(Submitter supplied) Objective. Microarray analysis was used to determine whether children with recent onset polyarticular juvenile idiopathic arthritis (JIA) exhibit biologically or clinically informative gene expression signatures in peripheral blood mononuclear cells (PBMC). Methods. Peripheral blood samples were obtained from 59 healthy children and 61 children with polyarticular JIA prior to treatment with second-line medications, such as methotrexate or biological agents. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

120 Samples

Download data: CEL

(Submitter supplied) Objective: A multi-center study of recent onset juvenile idiopathic arthritis (JIA) subjects prior to treatment with DMARDS or biologics was undertaken to identify peripheral blood gene expression differences between JIA subclasses and controls. Methods: PBMC from 59 healthy children and 136 JIA subjects (28 enthesitis-related arthritis[ERA], 42 persistent oligoarthritis, 45 RF- polyarthritis, and 21 systemic) were isolated on Ficoll. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

195 Samples

Download data: CEL

(Submitter supplied) To determine whether gene expression profiles from peripheral whole blood could be used to determine therapeutic outcome in a cohort of children with newly diagnosed polyarticular JIA.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL10558 GPL6884

112 Samples

Download data: TXT

(Submitter supplied) Identify biomarkers to predict response to therapy in polyarticular juvenile idiopathic arthritis (JIA) using gene expression microarrays.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

42 Samples

Download data: CEL

(Submitter supplied) Systemic Juvenile Idiopathic Arthritis (sJIA) has been strongly associated with macrophage activation syndrome (MAS). To better understand the pathogenesid of sJIA and to facilitate the search for MAS biomarkers, we examine gene expression profiles in untreated new onset sJIA. 17 new onset sJIA patients were included in the study. 5 of the 17 patients showed evidence of subclinical MAS and 2 eventually developed overt MAS. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

47 Samples

Download data: CEL

(Submitter supplied) We report whole blood gene expression of 12 healthy controls and 190 patients with either oligoarticular (n=43), polyarticular (n=46), or systemic JIA (n=26), or Crohn's disease (n=60) and ulcerative colitis (n=15). The subtypes of JIA are characterized by a gradient of differential gene expression ranging from controls to oligoJIA, polyJIA, sJIA, and IBD.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

202 Samples

Download data: TXT

(Submitter supplied) Canakinumab is a human anti-interleukin-1 beta (IL-1 beta) monoclonal antibody neutralizing IL-1 beta. Systemic juvenile idiopathic arthritis (SJIA) is a rare, multigenic, autoinflammatory disease of unknown etiology characterized by chronic arthritis; intermittent high-spiking fever, rash, and elevated levels of acute-phase reactants. Blood samples of SJIA patients were obtained from two phase 3 clinical trials conducted by the members of the Pediatric Rheumatology International Trials Organization (PRINTO) and the Pediatric Rheumatology Collaborative Study Group (PRCSG) (Clinicaltrials.gov: NCT00886769 and NCT00889863). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

206 Samples

Download data: CEL

(Submitter supplied) The objective of this study was to identify specific gene expression profiles able to predict the response of rheumatoid arthritis patients treated with methotrexate /abatacept (Aba). Thirty six RA patients were received Abatacept. The drug efficacy was evaluated with the DAS28 score after 6 months of treatment according to the EULAR response criteria. Among 36 Aba RA patients, 17 were responders and 19 were classified as no-responders. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

36 Samples

Download data: TXT

(Submitter supplied) We report the application of next-generation sequencing tehcnologies to profile the effects of tumor necrosis factor alpha (TNFα) treatment on the transcriptomes of cells derived from juvenile idopathic arthritis (JIA) patients and healthy control subjects. Whole blood from de-identified subects with JIA was collected following children's provided assent and parental signed consent. Controls included healthy adults under the age of 25 years without any medical conditions or family history of autoimmune disease. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

16 Samples

Download data: MTX, TSV

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL16791

70 Samples

Download data: GAPPEDPEAK, NARROWPEAK, TXT

(Submitter supplied) We used a multi-omics approach in an attempt to identify mechanisms driving the transcriptional abnormalities in peripheral blood CD4+ T cells of children with active JIA. We demonstrate that active JIA is associated with distinct alterations in CD4+ T cell chromatin, as assessed by ATAC-seq studies. However, 3D chromatin architecture, assessed by HiChIP and simultaneous mapping of CTCF anchors of chromatin loops, reveals that normal 3D chromatin architecture is largely preserved in JIA CD4+ T cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

16 Samples

Download data: BED, GAPPEDPEAK, TXT

(Submitter supplied) We used a multi-omics approach in an attempt to identify mechanisms driving the transcriptional abnormalities in peripheral blood CD4+ T cells of children with active JIA. We demonstrate that active JIA is associated with distinct alterations in CD4+ T cell chromatin, as assessed by ATAC-seq studies. However, 3D chromatin architecture, assessed by HiChIP and simultaneous mapping of CTCF anchors of chromatin loops, reveals that normal 3D chromatin architecture is largely preserved in JIA CD4+ T cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

32 Samples

Download data: TXT

(Submitter supplied) We used a multi-omics approach in an attempt to identify mechanisms driving the transcriptional abnormalities in peripheral blood CD4+ T cells of children with active JIA. We demonstrate that active JIA is associated with distinct alterations in CD4+ T cell chromatin, as assessed by ATAC-seq studies. However, 3D chromatin architecture, assessed by HiChIP and simultaneous mapping of CTCF anchors of chromatin loops, reveals that normal 3D chromatin architecture is largely preserved in JIA CD4+ T cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

22 Samples

Download data: NARROWPEAK

(Submitter supplied) Association of juvenile spondyloarthritis (jSpA) with the HLA-B27 genotype is well established, but there is little knowledge of other genetic factors with a role in disease development. The aim of the present study was to identify and confirm gene signatures and novel biomarkers in various cohorts of untreated and treated patients diagnosed with jSpA and other forms of juvenile idiopathic arthritis (JIA). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

15 Samples

Download data: CEL

(Submitter supplied) Severe asthma is a collection of disease entities with varying pathophysiological characteristics (7) that result in symptoms of cough, wheeze and breathlessness, with frequent exacerbations. To address the problem of phenotypic difference and heterogeneity, the Unbiased Biomarkers for the Prediction of Respiratory Disease Outcomes (U-BIOPRED) project was set up as a public-private partnership within the framework of the Innovative Medicines Initiative (IMI), engaging academia, the pharmaceutical industry and patient groups. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13158

498 Samples

Download data: CEL