I performed real-time PCR to find out the expression of different genes in osteoarthritis and normal rat model and for that, I used GAPDH as a standard. The issue I am facing is that the GAPDH expression in Osteoarthritis is low while its high in the normal model. I am confused as its a housekeeping gene so why its expression is not the same?
I recommend reading Vandesompele, J., De Preter, K., Pattyn, F., Poppe, B., Van Roy, N., De Paepe, A. and Speleman, F., 2002. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome biology, 3(7), pp.research0034-1. This landmark paper discusses the issue of housekeeping gene expression variability and provides a solution (geometric mean of multiple housekeeping genes).
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