ChIP on chip amplification problems - (Jun/16/2009 )
Another thought - how many cycles of WGA amplification are you doing?
I realize the last reply here was written 3 years ago but maybe we can restart it. My first question is of course if you manage to solve the problem? I am encountering the same problem right now and I do not really know how to deal with it. As for you my input (and sometimes one of my IPs) gives a nice output from the WGA2-kit but far from all of them. As Clare says my amounts post ChIP are also to low for the NanoDrop so I just take as much as I can (10 ul). When I look at my qPCR-runs the %-input is very low even though my control genes look fine so I have just imagined that it would be a matter of inefficient ChIP, but maybe the problem could be solved on a different level?