Restriction enzyme qPCR and dPCR. Correlation between expected and observed percent methylation for Methylation Dependent Restriction Enzyme (MDRE) (A,C) and Methylation Sensitive Restriction Enzyme (MSRE) (B,D) qPCR (A,B) and dPCR (C,D) analysis. Correlation performed with samples which comprise the optimal working range of the respective enzyme classes: 0-50% for MSRE (B,D) and 50-100% for MDRE (A,C) (dotted lines). Data points that were outside the viable range of the assay (< 0% or > 100% methylation) were removed from the analysis. All experimental conditions were n = 3 with the exception of the following which were n = 2: 10% and 25% MDRE qPCR and 90% MSRE qPCR (expected % methylation). Error bars show ± Standard Deviation of three independent replicate measurements. (E) Correlation between RE qPCR vs. dPCR measurements using the data points in which the restriction enzymes are within their optimal working range. A single outlying data point was removed from the correlation analysis. All correlations were significant at p < 0.0001 except for expected vs. MDRE dPCR which was p = 0.0011.