I'm considering using the Zymo Methylated & Non-methylated pUC19 DNA Set for use in my bisulfite sequencing experiments, but I'm not entirely sure how it works as an internal control. Any insight would be very much appreciated!
I guess that the Zymo Methylated & Non-methylated pUC19 DNA has not been bisulfite treated, am I right? If yes, you include them in your bisulfite treatment step as additional samples to your own DNA. After the treatment, you amplify the control DNAs as well as your own DNA. If you are going to do MSP, the unmethylated and methylated control DNA should give you predictable PCR results. This control for the success of the modification step because bisulfite modification can have problems of incomplete conversion and over conversion.