Recently I am doing CHIP-qPCR to test one TF binding. I use 10% of sample as Input and the rest 90% to do IP. I have the TF-positive cell line A and TF-depleted cell line B.
Primer is flanking the targeting site of TF.
The result I have is:
In A: Ct in IP 26 & Ct in Input 20 [Ct difference is 4]
In B: Ct in IP 30 & Ct in Input 20. [Ct difference is 10]
It seems TF binds to the targeting site.
However, I followed the calculation process of other people to estimate yield:
1/9*1/(2^6)
which is extremely low.
I am wondering if anybody has some idea about this: is it reasonable to do calculation like this? What is the average yield you get?