Fig. 2

Experimental versus tissue methylation differences. a Box plots of CG methylation distribution within methylated exons in each of the developmental stages separated for experiment 1 (left box of each sample) and experiment 2 (right boxes). Methylated exons have a minimum 10% average methylation in either of the experiments. b Density scatter plots of methylation level in methylated exons (defined in a) correlated between biological replicates. r is Pearson correlation coefficient value (p < 10⁻⁴). c PCA based on methylation level in methylated exons from all replicates. Samples are clustered to experiments (PC1) and tissues (PC2). d Hierarchical clustering of methylation in methylated exons of all replicates. Heatmap scale of fractional methylation is stretched from 0 (yellow) to 1 (red). e Bar graphs show the number of exons methylated in embryo and the indicated sample only in one of the experiments (white bars) or one of the tissues (black bars). For example, the black bar in D. larva shows the number of exons methylated only in D. larva or in embryo (by comparing columns 1–2 to 3–4 in d), and D. larva’s white bar shows the number of exons methylated only in embryo and D. larva from experiment 1 or in embryo and D. larva from experiment 2 (by comparing columns 1 and 4 to columns 2–3 in d)