Genome-wide DNA methylation study of hip and knee osteoarthritic and healthy cartilage reveals embryonic organ and skeletal system morphogenesis as major pathways involved in osteoarthritis
ABSTRACT: 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. Bisulphite converted DNA from 5 hip osteoarthritic, 6 knee osteoarthritic and 7 hip healhty cartilage samples were hybridised to the Illumina Infinium HumanMethylation450 BeadChip array
Evidence suggests that epigenetics plays a role in osteoarthrits (OA). The aim of the study was to describe the genome wide DNA methylation changes in hip and knee OA and identify novel genes and pathways involved in OA by comparing the DNA methylome of the hip and knee osteoarthritic cartilage tissues with those of OA-free individuals.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 col ...[more]
Project description: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). Keywords: Methylation profiling by array Overall design: Bisulphite converted DNA from the 97 samples were hybridised to the Illumina Infinium HumanMethylation450 BeadChip array.
Project description:Genome wide DNA methylation profiling of Neurons derived from human induced pluripotent stem cells (iCell Neurons) at different time points were abtained by the Infinium HumanMethylation450 BeadChip (450K array) Kit (WG-314-1002), which interrogates >480,000 CpG sites in the human genome.In total, 36 samples were profiled using the 450K arrays. 1 ug purified DNA from each timepoint was submitted to the University of Chicago Genomics Core where it was converted with the EZ-96 DNA Methylation™ Kit (Deep Well Format), as per manufacturer's protocol, followed by array analysis using the Infinium HumanMethylation450 BeadChip (450K array) Kit (WG-314-1002), which interrogates >480,000 CpG sites in the human genome.
Project description: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. Samples included 18 healthy controls and 23 OA patients. Bisulphite converted DNA from the 31 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2
Project description:Genome-wide DNA methylation profiling of peripheral blood mononuclear cells from 30 male offspring from the Yucheng (perinatal polychlorinated biphenyls and polychlorinated dibenzofurans exposure) cohort and 30 male offspring from the Yucheng' neighborhood referents with similar backgrounds. The Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across appromixmately 480,000 CpGs. Overall design: Genomic DNA was bisulfite-converted using the EZDNA Methylation-Gold Kod (Zyno Research) and analysed using the Infinium HumanMethylation450 BeadChip (Illumina) following manufacturer's instructions.
Project description:The pathogenesis of necrosis of femoral head (NFH) remains elusive now. Limited studies were conducted to investigate the molecular mechanism of hip articular cartilage damage of NFH. We conducted a genome-wide gene expression profiling of hip articular cartilage with NFH. Hip articular cartilage specimens were collected from 12 NFH patients and 12 healthy controls. Gene expression profiling of NFH articular cartilage was carried out by Agilent Human 4x44K Gene Expression Microarray chip. Differently expressed genes were identified using the Significance Analysis of Microarrays (SAM) software.
Project description:The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs in a total of 96 samples, including 8 hyperplasias, 33 endometrial cancers and 53 metastases, as well as 2 cell-lines. Bisulphite converted DNA from the 96 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
Project description:Human cartilage taken from young normal knees following anterior cruciate ligament repair and osteoarthritic cartilage; old normal (protected) and old osteoarthritic (unprotected) following total knee arthroplasty. Total RNA extracted using mirVana miRNA isolation kit (Life Technologies). The Affymetrix Flash Tag labelling kit was used to prepare samples for hybridisation onto Affymetrix miRNA 4.0 arrays.
Project description:Genome wide methylation profiling of BM-MSC derived from AML patients in comparison to healthy donor controls using Illumina Infinium HumanMethylation450 Beadchip bisulfit converted genomic DNA extracted from BM-MSC samples (AML n=32) and healthy donor controls (n=12) were hybridized onto an Illumina Infinium HumanMethylation450 Beadchip
Project description:Epigenome-wide association study (EWAS) of oral rinse samples from a cohort of 82 oral squamous cell carcinoma (OSCC) patients. The Illumina Infinium HumanMethylation450 Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in oral rinse samples. Bisulphite lsconverted DNA from the 82 oral rinse samples were hybridized to the Illumina Infinium HumanMethylation450 Beadchip