GSM6031047: MP46-1-OxBS; Homo sapiens; Bisulfite-Seq
Genomic DNA was extracted using QIAamp DNA Mini kit, and quality controls were achieved using a Nanodrop ND1000 to evaluate DNA purity and Qubit™ dsDNA BR/HS Assays to evaluate double strand DNA concentration Whole genome DNA methylation analysis was carried out with a Cambridge Epigenetics kit (TrueMethyl kit) that corresponds to an oxidative bisulfite reaction, to identify and analyze only 5-methylcytosine (5-mC). Briefly 400ng of genomic DNA were used to first perform an oxidation reaction, that converts 5-hydroxymethylcytosine (5-hmC) to 5- formylcytosine(5fC), thus after a bisulfite conversion, unmodified C and 5FC will be converted into uracils and sequenced as thymines contrary to 5mC that remains sequence as a cytosine Libraries were sequenced on an Illumina Hiseq as paired end 100bp for methylation analysis to identify Differenetial Methylated Region (DMR) between UM model vs NM.