This is a common problem and has been asked many times on this forum before. You need to add 1-2 ul DNase to your sample. Even sonication won't help you. But if you do all your work on ice you are less likely to see that gooey clump.
Cool, and the np40 doesn't hinder the DNAse? Also, to make myself clear I'm collectin supernatant and not the nuclear pellet. Thanks!