ChIP _ genomic DNA isolation - (Apr/05/2007 )
I'm trying to setup conditions for ChIP in plants and I'm having trouble with the initial purification of the genomic DNA. My problem is that the DNA seem to be already sheared before I even sonicate it ! When I run samples of before and after sonciation on an agarose gel, I see a super intense band at -700bp in BOTH sample. I've treated the samples with RNase but the band is still there so its probably not RNA. Anybody have a suggestion of what the problem is ?
Did you ever figure this out? I see a similar problem, although I'm using Xenopus tissues. I always get a bright 300bp band after RNAse and proteinase treatment.