GEO DataSets

(Submitter supplied) The aim of this study was to identify DNA methylation patterns in femur trabecular bone and cartilage of adult baboons (n=28 with knee OA, n=28 without knee OA). The Illumina Infinium MethylationEPIC Array was used to assess these genome-wide methylation patterns.

Organism:

Homo sapiens; Papio sp.

Type:

Methylation profiling by array

Platform:

GPL21145

112 Samples

Download data: CSV, IDAT

(Submitter supplied) The aim of this study was to identify DNA methylation patterns in femur trabecular bone and cartilage of age-matched female baboons, five with and five without knee osteoarthritis. The Illumina Infinium Human Methylation450 BeadChip was used to assess these genome-wide methylation patterns.

Organism:

Papio sp.; Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL16304

20 Samples

Download data: CSV, IDAT

(Submitter supplied) Cartilage samples were collected from hip or knee joint replacement patients either due to primary OA or hip fractures as controls. DNA was extracted from the collected cartilage and assayed by Illumina Infinium HumanMethylation450 ‎BeadChip array, which allows for the analysis of >480,000 CpG sites.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

18 Samples

Download data: IDAT, TXT

(Submitter supplied) Genome wide gene expression was determined in paired samples of OA affected and preserved cartilage of the same joint using microarray analysis for 33 patients of the RAAK-study. Among the 1717 genes that were significantly different expressed between OA affected and preserved cartilage we found significant enrichment for genes involved in skeletal development (e.g. TNFRSF11B and FRZB). Also several inflammatory genes such as CD55, PTGES and TNFAIP6, previously identified in within-joint analyses as well as in analyses comparing preserved cartilage from OA affected joints versus healthy cartilage were among the top genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

73 Samples

Download data: TXT

(Submitter supplied) The aim of this study was to characterise the genome-wide DNA methylation profile of osteoathritis (OA) chondrocytes from both knee and hip cartilage, providing the first comparison of DNA methylation between OA and non-OA hip cartilage, and between OA hip and OA knee cartilage. The study was performed using the Illumina Infinium HumanMethylation450 BeadChip array. Genome-wide methylation was assesed in chondrocyte DNA extracted from 23 OA hip, 73 OA knee and 21 healthy hip controls (NOF - neck of femure samples). more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

97 Samples

Download data: IDAT, TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Platforms:

GPL11532 GPL8490

64 Samples

Download data: CEL

(Submitter supplied) The aim of this study is to identify, for the first time, the genome-wide DNA methylation profiles of human articular chondrocytes from OA and healtly cartilage samples. Genome wide DNA methylation profiling of normal and osteoarthritic samples. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in cartilage knee samples. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

41 Samples

Download data: TXT

(Submitter supplied) The aim of this study is to identify, for the first time, the genome-wide DNA methylation profiles of human articular chondrocytes from OA and healtly cartilage samples. A subsequent validation of methylation profiles were performed in an idependent cohort of OA samples with Affymetrix Hugene 1.1 st array This represents the gene expression component of the study only

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL11532

23 Samples

Download data: CEL

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

Organism:

Chlorocebus aethiops; Macaca mulatta; Pan troglodytes; Homo sapiens; Callithrix jacchus; Papio sp.

Type:

Methylation profiling by array

Platform:

GPL21145

116 Samples

Download data: IDAT

(Submitter supplied) The aim of this study was to characterize the genome-wide DNA methylation profiles of marmoset femur trabecular bone samples (n=6) and identify how they relate to aspects of femur bone morphology. The Illumina Infinium MethylationEPIC Array was used to assess these genome-wide methylation patterns.

Organism:

Callithrix jacchus; Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

6 Samples

Download data: CSV, IDAT

(Submitter supplied) The aim of this study was to characterize the genome-wide DNA methylation profiles of nonhuman primate trabecular bone samples (n=58), identify how they relate to aspects of femur bone morphology, and assess how these epigenetic patterns vary between taxa. The Illumina Infinium MethylationEPIC array was used to assess genome-wide methylation patterns.

Organism:

Callithrix jacchus; Macaca mulatta; Homo sapiens; Papio sp.; Chlorocebus aethiops; Pan troglodytes

Type:

Methylation profiling by array

Platform:

GPL21145

58 Samples

Download data: CSV, IDAT

(Submitter supplied) The aim of this study was to characterize the genome-wide DNA methylation profiles of vervet femur trabecular bone samples (n=10) and identify how they relate to aspects of femur bone morphology. The Illumina Infinium MethylationEPIC Array was used to assess these genome-wide methylation patterns.

Organism:

Homo sapiens; Chlorocebus aethiops

Type:

Methylation profiling by array

Platform:

GPL21145

10 Samples

Download data: CSV, IDAT

(Submitter supplied) The aim of this study was to characterize the genome-wide DNA methylation profiles of adult baboon femur trabecular bone samples (n=28) and identify how they relate to aspects of femur bone morphology. The Illumina Infinium MethylationEPIC Array was used to assess these genome-wide methylation patterns.

Organism:

Homo sapiens; Papio sp.

Type:

Methylation profiling by array

Platform:

GPL21145

28 Samples

Download data: CSV, IDAT

(Submitter supplied) The aim of this study was to characterize the genome-wide DNA methylation profiles of macaque femur trabecular bone samples (n=10) and identify how they relate to aspects of femur bone morphology. The Illumina Infinium MethylationEPIC Array was used to assess these genome-wide methylation patterns.

Organism:

Macaca mulatta; Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

10 Samples

Download data: CSV, IDAT

(Submitter supplied) We report an immortalised CRISPR-Cas9 mesenchymal stem cell line knockdown of Plectin, we initally noted that patients with osteoarthritis association single nucelotide polymorphism rs11780978 had a correlation between genotype at rs11780978 and allelic expression imbalance, with a reduced expression of Plectin from the risk allele. We replicated the effect of the risk allele by deleting 26bp from exon 3 of Plectin to generate multiple knockdown lines to assess the molecular phenotype of Plectin knockdown in the cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

7 Samples

Download data: TXT

(Submitter supplied) Osteoarthritis (OA) is a polygenic disease of older people resulting in the breakdown of cartilage within articular joints. Although a leading cause of disability, there are no disease-modifying therapies. Evidence is emerging to support the origins of OA in skeletogenesis. Whilst methylation QTLs (mQTLs) co-localizing with OA GWAS signals have been identified in aged human cartilage and used to identify effector genes and variants, such analyses have never been conducted during human development. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

22 Samples

Download data: BW

(Submitter supplied) Osteoarthritis (OA) is a chronic disease of the joint characterized by a progressive degradation of articular cartilage and subchondral bone. In healthy tissue, specialized cells called chondrocytes are regulating a balanced cartilage catabolism and anabolism. By contrast osteoarthritic joints are characterized by a dramatic increase of cartilage catabolism, due to changes of gene expression patterns within chondrocytes. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL17387

10 Samples

Download data: TXT

(Submitter supplied) Autologous chondrocyte transplantation (ACT) is a routine technique to regenerate focal cartilage lesions. However, patients with osteoarthritis (OA) are lacking an appropriate long-lasting treatment alternative, partly since it is not known if chondrocytes from OA patients have the same chondrogenic differentiation potential as chondrocytes from donors not affected by OA. Articular chondrocytes from patients with OA undergoing total knee replacement (Mankin Score >3, Ahlbäck Score >2) and from patients undergoing ACT, here referred to as normal donors (ND), were isolated applying protocols used for ACT. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3758

Platform:

GPL570

12 Samples

Download data: CEL, EXP

Analysis of monolayer cultures and Hyaff-11 scaffold cultures of chondrocytes from 3 donors suffering from osteoarthritis (OA). Results provide insight into the differentiation process of OA chondrocytes and their possible use in matrix-associated autologous chondrocyte transplantation (ACT).

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 disease state, 2 growth protocol sets

Platform:

GPL570

Series:

GSE16464

12 Samples

Download data: CEL, EXP

(Submitter supplied) We employed Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) to map the accessible chromatin landscape in articular knee cartilage of OA patients. We identified 109,215 accessible chromatin regions for cartilages, of which 71% were annotated as enhancers. By overlaying them with genetic and DNA methylation data, we have determined potential OA-relevant enhancers and their putative target genes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

16 Samples

Download data: BIGWIG