During my initial chip experiments I was not measuring the amount of DNA in each qPCR reaction. I started with same amounts of chromatin during IP and after crosslinking I recovered the DNA in equal volumes of buffer. Out of curiosity I quantified the DNA conc and I have vastly different amounts between samples (not too surprising, really). How does this impact my results? What concentration should I be using?
Thanks for the help -- so far I have some nice prelim results but I am trying to make sure I'm doing everything correctly
