ChIP in WT and KO cells - how to analyze - (Feb/01/2010 )

I am doing ChIP on cells as follows:

WT
WT + inducer
KO
KO + inducer

My problem is that I don't know how to properly compare them. I sonicated and did ChIP all on the same day, so they are from the same experiment. Should I use percent input, or IP/mock? Percent input doesn't seem right to me, but neither does IP/mock. I am driving myself crazy trying to figure this out!

Thanks in adance!

I would suggest %input, primarily because, at least in my case, my Ct values for mock tend to be very variable and thus I don't necessarily trust them much to use in comparisons (perhaps your mock Ct values are more consistent?). Although, I have seen both in the literature so it appears that both are accepted ways for doing the analysis.

As for statistical analysis, I would suggest a 2 X 2 (Genotype X Inducer) ANOVA on whatever it is you choose (%input or IP/mock) to get the most statistical power.

MM