Fig. 3

The majority of uniquely methylated cytosines in ESC total poly(A) RNA are due to differential methylation rather than differential expression between ESC and brain. a The expression levels and methylation rates of m5Cs identified as unique to ESCs were analyzed in the brain samples. b The expression levels and methylation rates of m5Cs identified as unique to brain were analyzed in the ESC samples. Multi-level pie charts display the numbers of sites on annotated and non-annotated transcripts in the innermost ring, the numbers of sites on transcripts with a mean normalized count of more (dark green) or fewer (light green) than 10 reads in the middle ring, and the numbers of sites with sequence coverage <10 reads (blue) or sequence coverage >10 reads but methylation rate lower than 0.2 (yellow) in the outer ring. Positions in which the mean values for coverage and non-conversion were skewed towards methylation by an individual replicate were classified as biased mean