i performed a real time PCR. I was looking for expression fold changes for 2 genes and i had two sample pools, one treated and the other not treated (for each gene). The problem is that my housekeeping gene (UBQ 30) got a fold change on the treatment. Therefore, what is the correct interpretation and data treatment?
i mean, is it correct to use each control and treatment i got for UBQ CT values to normalize the other two genes corresponding CT, as housekeeping genes are "by definition" expected not to change? (and that is why indeed they are used to normalize)
or should i rather make a mean of my whole UBQ CT-s and normalize all other genes CT values with that mean?