Enzymatic shear vs sonication - (Aug/01/2010 )
I'm new to ChIP and have only tried enzymatic shearing so far (from activemotif). I was wondering if anyone has tried both methods and can give a take on them.
Using the enzymatic shearing kit, 200ul sheared DNA per IP and resuspending the extracted DNA in 100ul water, the positive control Ct was 28 (I used 5ul per PCR reaction). I'm guessing sonication might give me a better yield?
I've never used both, just sonication. But from the folks I've talked to that have used enzymatic shearing, they say you get much smaller fragment sizes than in sonication, even with very brief enzyme exposure. So I guess if you know exactly what you're looking for then enzymatic shearing would be fine. If you want a larger "target" then sonication might be better...just a thought