Real-time PCR was used to measure the representation of four different loci in 10 ng bisulfite converted DNA, before (–WBA) and after (+WBA) amplification with the EpiTect Whole Bisulfitome Kit. DNA was first bisulfite converted using either the EpiTect Bisulfite Kit or a kit from supplier Z, and was then amplified; qPCR was performed using the QuantiTect SYBR® Green PCR Kit. In the EpiTect converted DNA, the four loci were represented similarly before and after amplification. Higher CT values for the DNA converted with the competitor’s bisulfite kit indicate higher DNA fragmentation prior to WBA. Following amplification, the relative representation of the four loci was increased and different, indicating lower whole bisulfitome amplification and unequal amplification.
A starting amount of 50 ng bisulfite converted DNA was used for the whole bisulfitome amplification reaction. The amplification was performed using the EpiTect Whole Bisulfitome Kit, as well as kits from suppliers A and S. DNA yields following the amplification reactions were measured with PicoGreen. The EpiTect Whole Bisulfitome Kit resulted in a 50-fold increase in DNA yield, which was much higher than the yields from the other suppliers' kits.