GSE61968
Semiconductor-based sequencing of genome-wide DNA methylation states
Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) is a widely used  approach to study DNA methylation genome-wide. Here, we present a novel MeDIP-Seq  protocol compatible with the Ion Torrent semiconductor-based sequencing platform that  is scalable and accurately identifies sites of differential DNA methylation. Additionally,  we demonstrate that the high-throughput data derived from MeDIP-Seq on the Ion  Torrent platform provides adequate coverage of CpG cytosines, the methylation states  of which we validated at single-base resolution on the Infinium HumanMethylation450K  Beadchip array. We applied this integrative approach to further investigate the role of  DNA methylation in alternative splicing and to profile 5-mC and 5-hmC variants of DNA  methylation in normal human brain tissue that we observed localize over distinct  genomic regions. These applications of MeDIP-Seq on the Ion Torrent platform have  broad utility and add to the current methodologies for profiling genome-wide DNA  methylation states in normal and disease conditions. Overall design: MeDIP-Seq on Ion Torrent Platform in HCT116 and Human Brain