Are you using the right reference genes?
Considering Real-Time PCR for gene expression analysis? Have you tested multiple reference genes or are you just going to run with your favorite such as 18S? Check out this article on suitable reference gene selection before you move forward. It could save you lots of grief in the long run.
Suitable reference genes for real-time PCR in human HBV-related hepatocellular carcinoma with different clinical prognoses
Li-Yun Fu et al. BMC Cancer 2009, 9:49
Housekeeping genes are routinely used as endogenous references to account for experimental differences in gene expression assays. However, recent reports show that they could be de-regulated in different diseases, model animals, or even under varied experimental conditions, which may lead to unreliable results and consequently misinterpretations. This study focused on the selection of suitable reference genes for quantitative PCR in human hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) with different clinical outcomes.
Fu, L., Jia, H., Dong, Q., Wu, J., Zhao, Y., Zhou, H., Ren, N., Ye, Q., & Qin, L. (2009). Suitable reference genes for real-time PCR in human HBV-related hepatocellular carcinoma with different clinical prognoses BMC Cancer, 9 (1) DOI: 10.1186/1471-2407-9-49