Project description:Genome wide DNA methylation profiling of three normal (N) and eight ulcerative colitis (UC) samples as well as one human colon cancer cell (HCT116) . The Illumina Infinium 450k Human DNA methylation platform was used to obtain DNA methylation profiles across approximately 480,000 CpGs.
Project description:Genome wide DNA methylation profiling of individuals across a large age range. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450k CpGs from human whole blood.
Project description:Genome wide DNA methylation profiling of human medulloblastoma. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs. Preprocessed data performed using Illumina normalization in the minfi package as described in Sturm et al, Cancer Cell, 2012.
Project description:Genome wide DNA methylation profiling of human medulloblastoma. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs. Preprocessed data performed using Illumina normalization in the minfi package as described in Sturm et al, Cancer Cell, 2012. Bisulphite converted DNA from the 91 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2
Project description:Abstract The proper identification of differentially methylated CpGs is central in most epigenetic studies. The Illumina Human Methylation 450k BeadChip is widely used to quantify DNA methylation, nevertheless the design of an appropriate analysis pipeline faces severe challenges due to the convolution of biological and technical variability and the presence of a signal bias between Infinium I and II probe design types. Despite recent attempts to investigate how to analyze DNA methylation data with such an array design, it has not been possible to perform a comprehensive comparison between different bioinformatics pipelines due to the lack of appropriate datasets having both large sample size and sufficient number of technical replicates. Here we perform such a comparative analysis, targeting the problems of reducing the technical variability, eliminating the probe design bias and reducing the batch effect by exploiting two unpublished datasets, which included technical replicates and were profiled for DNA methylation either on peripheral blood, monocytes or muscle biopsies. We evaluated the performance of different analysis pipelines and demonstrated that a) it is critical to correct for the probe design type, since the amplitude of the measured methylation change depends on the underlying chemistry; b) the effect of different normalization schemes is mixed, and the most effective method in our hands were quantile normalization and Beta Mixture Quantile dilation (BMIQ); c) it is beneficial to correct for batch effects. In conclusion, our comparative analysis using a comprehensive dataset suggests an efficient pipeline for proper identification of differentially methylated CpGs using the Illumina 450k arrays. DNA samples from peripheral blood or CD14+ monocytes were included in the study. DNA methylation levels were profiled using Illumina 450K arrays. Specifically, 50 biological sample replicates from PB and 36 biological sample replicates from monocytes were randomly assigned to 8 BeadChips with technical replicates and processed in one run (a total of 96 DNA samples). Eight samples were technically replicated in pairs, while one sample was represented in a trio of replicates. Different analysis pipelines were compared, however, the file uploaded refers to the best scored. In our publication we used this one to make all analyses and conclusions.
Project description:Genome wide DNA methylation profiling of individuals across a large age range. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450k CpGs from human whole blood. Bisulphite converted DNA from the 656 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
Project description:Genome wide DNA methylation profiling of HSTL in comparison to benign T-cell subsets. The Illumina Infinium 450k Human DNA methylation Beadchip was used.
Project description:Genome wide DNA methylation profiling of ependymomas. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,500 CpGs. Samples included 83 ependymomas.
Project description:Genome wide DNA methylation profiling of 3 patient-derived colorectal cancer samples with different CIMP profiles. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs
Project description:Genome wide DNA methylation profiling of 12 paired monozygotic twin samples. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in 12 paired monozygotic twin samples.
