since there is available commercial kits to extract total MeDNA, is it possible to evaluate how much a gene is methylated using MeDNA isolation kits then real time-PCR ?
I am not expert in this area, but I am still throwing the answer. Someone with real experience will be forced to answer soon.
In my view, you may start with two duplicate sample, in one you isolate DNA and do DNA methylation, in second, you isolate RNA and make cDNA and do qPCR. You may do comparison between groups you are interested in.