ChIP crosslinking question - (Mar/23/2011 )
Hi all. Our lab just started doing ChIP assays. We're using both a slightly modified fast ChIP protocol and an EZ-Chip Kit, and sonicating with Episonic 1000. But I just have a quick question about crosslink efficiency -- how does one go about determining whether there was good crosslinking efficiency achieved? Would I be able to sonicate crosslinked samples and un-crosslinked samples and then check the gels for comparison in smears/fragment sizes? Does that even make sense?
There is no easy way of checking cross linking efficiency. If you just follow the standard protocol the efficiency should be good enough. If your experiment requires stronger cross linking, you can increase crosslinking duration, but it will make your reverse crosslinking harder.