I'm working on both 2D and 3D mammalian cell culture (with different scaffolds) and I compare genes expression with qPCR but It's quite difficult to find relevant housekeeping genes. Of course I'm not using cytoskeleton-linked genes (for 2D and 3D comparison) but metabolism genes expression (like GAPDH) also shown significant variation. I'm trying ribosomal proteins but their expression seem to be modified by culture conditions.
Hi Guillaume, our lab has compared a number of different housekeeping genes and found RPL13a as the most reliable one.
Article Ribosomal Protein L13a as a Reference Gene for Human Bone Ma...
There is at least not with certainty a universal one in Arabidopsis (Wallström et al. 2010 Plant Sci 183: 190-196). Reference gene quantification can lead you very wrong. Unless you are comparing very different materials, it may be best to standardise by RNA amount, and include some "housekeeping genes" as controls. If you have to use them, do "reference gene validation".
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