Fig. 2.

Use of RRBS data in identifying DNA methylation in promoters of genes of interest. (A) DNA methylation data for Dnmt1 promoter in ESCs and neurons from R1 and Tet/Tet cells viewed in UCSC browser. (B) Validation of DNA methylation data by Combined Bisulfite Restriction Analysis (COBRA). Agarose gel electrophoresis of bisulfite PCR products obtained from biological replicates of ESCs and neurons from R1 and Tet/Tet cells using primers for the indicated 288 bp region. +: reaction mixture was incubated with BstUI enzyme, -: no enzyme control. The presence of a faint 165 bp fragment confirms presence of methylated CpGs in the analyzed genomic region in the DNA from Tet/Tet neurons.