450 k methylation chip

Extraction of genomic DNA was performed by the phenol-chloroform method [20 ], after which it was bisulfite converted using the EZ DNA Methylation – GoldTM kit (ZymoResearch, USA). The bisulfite converted DNA was hybridized to the Illumina 450 k methylation chip (Illumina, San Diego, CA, USA) to measure DNA methylation in 485 577 individual CpG sites. In the discovery group, DNA obtained from blood samples taken from the same individual before and six months after surgery were hybridized to the same physical chip. The array was imaged using the Illumina iScan system (Illumina, San Diego, CA, USA), determining the percentile methylation for each CpG site across the study groups.

Genomic DNA was extracted using the phenol-chloroform method [11 ]. Bisulfite conversion was performed with the EZ DNA Methylation—Gold kit (Zymo research. Cat. No. D5004). The degree of DNA methylation was determined by the Illumina 450K methylation chip (Illumina, San Diego, USA). After the bisulfite converted DNA was hybridized to the array, fluorescence was measured using the Illumina iScan system. The raw data were processed using GenomeStudio 2009–2. Blood samples from each subject were hybridized to the same physical chip to minimize biases. Note that one subject of an initial sample of 12 obese humans was not considered eligible for analysis because of technical failure during the methylation profiling procedure.