Project description:Design, annotation, and technical and biological validation of the MouseMethylation Beadchips (MM285) platform. Application of the mouse array for tissue and tumor epigenetics, comparative epigenomics, genomic imprinting, epigenetic inhibitors, PDX assessment, backcross tracing, and epigenetic clocks.
Project description:In this study, the Infinium BeadChip DNA methylome profiling technology was optimized for suboptimal input DNA conditions, including ultra-low input down to single cells. We acquired knowledge on the boundaries and limits of the Infinium DNA methylation BeadChips with suboptimal input DNA. These findings offer comprehensive solutions to expand the application of this technology to cases with limited DNA.
Project description:We compared the global DNA methylation levels of hairless mouse epidermis using the Infinium Mouse Methylation BeadChip from Illumina and whole genome bisulfite sequencing (WGBS). We also studied the effect of sample storage conditions by using fresh and fresh-frozen epidermis. The DNA methylation levels of xxx,xxx CpG sites covered by both the BeadChip and WGBS were compared. DNA methylation levels obtained with WGBS and the BeadChip were strongly correlated (Pearson correlation r = 0.984). We applied a threshold of 15 reads for the WGBS methylation analysis. Even at a threshold of 10 reads, we observed no substantial difference in DNA methylation levels compared with that obtained with the BeadChip. The DNA methylation levels from the fresh and the fresh-frozen samples were strongly correlated when analysed with both the BeadChip (r = 0.996) and WGBS (r = 0.994). We conclude that the two methods of analysis generally work equally well for studies of DNA methylation of mouse epidermis and find that fresh and fresh-frozen epidermis can generally be used equally well. The choice of method will depend on the specific study’s aims and the available resources in the laboratory.
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:DNA methylation classification reference set (1077) and validation set (428) of 1505 sarcoma samples using Illumina HumanMethylation450 BeadChips or Illumina Infinium HumanMethylation850 BeadChips
Project description:Genome wide DNA methylation profiling of primary CNS lymphomas. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,500 CpGs. Samples included 95 primary CNS lymphomas and 2 metastatic DLBCLs in CNS.
Project description:Genome-scale DNA methylation was analyzed in a large cohort of pheochromocytomas and paragangliomas (PCC/PGL). Consensus clustering identified 3 stable clusters significantly associated with expression subgroups, gene mutations, and clinical parameters. Bisulfite-converted DNA from 145 fresh frozen PCC/PGL and 3 normal adrenal medulla samples were hybridized to Illumina Infinium 27k Human Methylation BeadChips.
Project description:We used the Illumina Infinium MethylationEPIC to measure DNA methylation in mouse liver samples. We identified 13,665 conserved probes and compared methylation signal with sequecing based data (MBD-seq and RRBS)
Project description:We compared the global DNA methylation levels of hairless mouse epidermis using the recently released Infinium Mouse Methylation BeadChip from Illumina and whole genome bisulphite sequencing (WGBS). We also studied the effect of sample storage conditions by using fresh and fresh-frozen epidermis. The DNA methylation levels of 123,851 CpG sites covered by both the BeadChip and WGBS were compared. DNA methylation levels obtained with WGBS and the BeadChip were strongly correlated (Pearson correlation r = 0.984). We applied a threshold of 15 reads for the WGBS methylation analysis. Even at a threshold of 10 reads, we observed no substantial difference in DNA methylation levels compared with that obtained with the BeadChip. The DNA methylation levels from the fresh and the fresh-frozen samples were strongly correlated when analysed with both the BeadChip (r = 0.999) and WGBS (r = 0.994). We conclude that the two methods of analysis generally work equally well for studies of DNA methylation of mouse epidermis and find that fresh and fresh-frozen epidermis can generally be used equally well. The choice of method will depend on the specific study's aims and the available resources in the laboratory