DNA in methylation analysis - (Apr/27/2012 )
I have a question for you, DNA isolation method can influence in the DNA methylation analysis?? For example if you use two different kits to isolate DNA, that could affect to the DNA methylation??
I would say no. Especially if you use commercially available kit. DNA is DNA.
The same goes for Bisulfite reaction (EpiTect or Zymo).
But that is just my opinion.
it is possible to get technical artefact due to inefficient removal of protein by your extraction method, if you are using a kit then generally it should be okay, but if your protienase K has gone off and you don't know it, well that is a problem.
The reply to your question will probably depend on what type of methylation analysis you are planning.
To give you an idea... we run a company that provides genome-wide methylation sequencing services and we have seen that there is a difference in the quality of the DNA for this specific application between different commercially available kits.
We always recommend our customers to use the easyDNA kit by Invitrogen.