We report a single-cell bisulfite sequencing (scBS-seq) method that can be used to accurately measure DNA methylation at up to 48.4% of CpG sites. Embryonic stem cells grown in serum or in 2i medium displayed epigenetic heterogeneity, with '2i-like' cells present in serum culture. Integration of 12 individual mouse oocyte datasets largely recapitulated the whole DNA methylome, which makes scBS-seq a versatile tool to explore DNA methylation in rare cells and heterogeneous populations.This work was supported by the UK Biotechnology and Biological Sciences Research Council grant BB/J004499/1, UK Medical Research Council grant MR/K011332/1, Wellcome Trust award 095645/Z/11/Z and EU FP7 EpiGeneSys and BLUEPRINT
