I am currently standardizing the ChiP protocol in my lab and very naive in the technique. I performed a ChiP protocol with a protein specific antibody and Igg control and after precipitation, I resuspended the pellet as well as 10% input sample in 100 microliters of water. I do not have bio analyzer so wasn't sure about the concentration of the precipitated DNA, but could get the concentration for 10% input sample. I diluted the 10% input to 1% input and used 4 microliters of input as well as precipitated DNA in the qPCR reaction. I used primer set-1 which should recognize the bound region versus the primer set- which lies 2kb outside of my protein of interest bound region. I can normalize it by Igg ct values, but don't understand how I can use the input Ct values. The input Ct values will always be much lower than the precipitated one so a simple normalization is not working. Can anyone suggest how to calculate the % input in this case?
Here are the Ct values:Wt-1%----33.8 Wt-Igg----40 Wt-SM1--39.3 WT-sm5--37.6
Thank you so much in advance!!