I have tried several housekeeping genes – Hprt, β-actin and GAPDH, to analyze the relative expression of a cytokine for measuring the inflammatory local response in mice ears. However, all these housekeeping genes show significant variation in both within and between different experimental conditions.
I really don't know how to solve this. I take the same amount of RNA (quantified by nanodrop) to make cDNA so I guess I have the same concentration in all the samples.
Any suggestion of what can happens and how to solve it? Could I use something different to measure the relative quantification? (My cytokine of interest is TNF).
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