Hello, I was hoping someone could help me figure out the issue I am having with sonicated DNA for ChIP Seq. I ran an initial sonication test in a bioruptor to optimize sheering size found that around 30 cycles looked to be in the right range (100-300bp) according to my agarose gel. To get a more accurate measure of the DNA size and quantity I ran the same samples on a high sensitivity DNA bioanalyzer chip but got very different results. While The DNA chip also picked up the smaller size fragments I saw on the agarose gel, it also showed a band smear near 1500-3000bp in nearly every sample (these bands were not present in the agarose gel). I don't think it is a sensitivity issue because the band on the DNA ChiP is equal to or greater than the concentration of the lower band. Has anyone ever seen this or know why I am getting to very different results?
Thanks
Mike
