Project description:Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling [HumanMethylation450]
Project description:We developed a comprehensive analysis pipeline to conduct Epigenome-wide Association Studies (EWAS) using the Illumina Infinium HumanMethylation450 BeadChip, based on data from 2,664 individuals, and 36 samples measured in duplicate. We propose new approaches to quality control, data normalisation and batch correction through control-probe adjustment, and demonstrate that these improve data-quality. Using permutation testing we establish a null hypothesis for EWAS, show how it can be affected by correlation between individual methylation markers and present methods to restore statistical independence. Bisulfite-converted DNA for 2,664 human samples and 36 technical replicates were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2.
Project description:Genome wide DNA methylation profiling of control (vector-transfected) and KLF4-overexpressing human podocytes (parental cell line: Saleem et al. JASN 13:630, 2002). The Illumina HumanMethylation450 Beadchip was used to obtain DNA methylation profiles.
Project description:Bisulphite (BS) and oxidative bisulphite (oxBS) converted DNA from 4 normal human placentas were hybridized to the Illumina HumanMethylation450 Beadchip v1.2, obtaining the BS and oxBS DNA methylation profiles across approximately 450,000 CpGs. By using the oxBS treatment, the selective chemical oxidation of 5-hydroxymethylcytosine (5hmC) to 5-formylcytosine (5fC) and the deamination of the latter to uracil during the BS conversion allowed the quantification of independent 5-methylcytosine (5mC) and 5hmC methylation levels at every single CpG. In consequence, this data set characterizes the genome-wide distribution of 5hmC in the human placenta offerring a high-confidence list of intervals enriched for 5hmC in this tissue.
Project description:Genome wide DNA methylation profiling of control (vector-transfected) and KLF4-overexpressing human podocytes (parental cell line: Saleem et al. JASN 13:630, 2002). The Illumina HumanMethylation450 Beadchip was used to obtain DNA methylation profiles. Bisulphite converted DNA samples from control (vector-transfected, n=1) and KLF4-overexpressing human podocytes (n=1) were hybridised to the Illumina HumanMethylation450 Beadchip and DNA methylation was compared.
Project description:Genome wide DNA methylation profiling of F-36P leukemic cells treated by arsenic disulfide, The Illumina HumanMethylation450 BeadChip was used to obtain DNA methylation profiles
Project description:Genome wide DNA methylation profiling of normal whole blood samples. The data consist of 43 samples with Illumina HumanMethylation450 BeadChip data.
