3 replies to this topic

[Mighty Mouse]

So this question was posted on the qPCR forum, but I figured it really belonged here. When running your mock ChIP samples in qPCR, what do you do about samples that show no amplification? If you run 40 cycles do you just put it in as a Ct value of 40? Or do you increase your cycles to 50 and typically get some sort of amplification?

[Prep!]

idealy 40 cycles are a very good measure of concluding if the template is present or not. Imagine 2 raised to 40 times doubling... still no signal shows up... u gottta stop being too optimistic!!! unlesss u are happy with even one copy of it and wanna extend it till u get a signal!!!

[Mighty Mouse]

Well my concern isn't that I really "want" to see a signal in my mock ChIP samples...my question is how to take it into account in my % input calculations for the mock samples. Do I just score it a Ct of 40?

[Prep!]

ya if u get no signal.. the Ct score is 40.. some platforms don giev a Ct value at all if the amplification is later than 35 cycles.