GSM1202747: ST_BiSeq_Rep2; Mus musculus; Bisulfite-Seq
DNA was extracted using Gentra PUREGENE DNA Isolation Kit and sheared on COVARIS to a median 400 bp fragment. For all samples unmethylated lambda DNA was added to 1% final concentration (Promega Madison, WI 53711). Methylated paired-end adapters were ligated to sheared DNA according to the Illumina library preparation protocol. Sodium bisulfite conversion was performed using the EpiTect Bisulfite Kit (Qiagen, Valencia, CA 91355) with an additional incubation step at 60C for 120 min to increase conversion rate. Bisulfite treated DNA was then PCR amplified with 16 cycles and sequenced. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.