Fig. 2

a Distribution of DNA methylation across the genome in 100-CpG windows in all samples compared to Germinal Vesicle (GV) oocytes from Shirane et al. [38]. b SeqMonk screenshot of a 1.7 Mb region of chromosome 11 depicting the hypermethylated (HyperD) and hypomethylated (HypoD) domains characteristic of the oocyte methylome in each of the 16 individual methylation datasets. Genes and oocyte mRNA are shown in red or blue depending on their direction of transcription (forward and reverse, respectively). Each color-coded vertical bar in the screenshot represents the methylation value of a non-overlapping 100 CpG tile. HypoD, HyperD, and oocyte mRNA annotation tracks are derived from Veselovska et al. [24]. c DNA methylation percentages at HyperD in all samples (n = 26,570). In the box:whiskers plot, the line across the middle of the box shows the median, the upper and lower extremities of the box show the 25th and 75th percentile of the set of data, and the upper and lower black whiskers show the median plus/minus the interquartile (25–75%) range multiplied by 2. Individual points which fall outside this range are shown as filled circles, and represent single outlier tiles. d Box:whisker plot showing the DNA methylation percentages at HypoD (n = 38,739). e DNA methylation percentages of CpG Islands (CGI) located at promoters (n = 11,542) and CGIs highly methylated in oocytes (n = 2014). Each point represents the mean value along with error bars indicating the 95% confidence interval for the measure. f Principal component analysis (PCA) of informative 100-CpG tiles (value between 0 and 100 in all 16 samples; n = 195,170) shows how biological replicates cluster together within each group and differently between conditions