MOESM3 of Targeted bisulfite sequencing of the dynamic DNA methylome

Additional file 3: Figure S2 a. Distribution of CpG level read coverage (x-axis) across 4 technical replicates of DyMe-Seq at different mean coverage levels indicated (e.g. R1, c=36.2, indicating a mean CpG coverage of 36.2 reads). Figure S2b. Distribution of the observed fraction of GC content across 200-bp tiles of the target DyMe-Seq capture set across 4 technical replicates of DyMe-Seq (R1-R4) at different mean coverage levels (see Figure S2a.) and the expected percentage based on analysis of target capture set. Figure S2c. Percentage of duplicate reads as a function of genomic DNA input in nanogram for DyMe-Seq using a standard “adapter-ligation first” library preparation method (KAPA). Error bars indicate standard error/range based on n≥2. Figure S2d. Percentage of duplicate reads as a function of genomic DNA input in nanogram for DyMe-Seq using a “bisulfite first” library preparation protocol (Swift). Error bars indicate standard error/range based on n≥2. Figure S2e. On-target rate for three independent DyMe-Seq experiments. On-target rate is defined as on and near (±250) bait bases divided by the number of passing filter bases aligned. Figure S2f. On-target rate for all DyMe-Seq experiments conducted in this study, giving a median On-target rate of 70.3%. Figure S2g. Left: Distribution of methylation level differences between two biological replicates of hESC WGBS dataset (y-axis) as a function of the methylation level in WGBS replicate R1 (x-axis) across 200-bp tiles of the DyMe-Seq target capture set. Right: This panel depicts the same distribution type of distribution as on the left, but now shows the methylation level differences between WGBS replicate R1 and a DyMe-Seq dataset for a different biological replicate of hESCs, again condition on the methylation level in WGBS hESC replicate 1