I have been trying 18S and U6 as internal control. I found that they increase significantly with my treatment. What other internal controls are good especially for mouse.
Thank you
i have used beta actin, 18s, gapdh, and beta actin has always been the most reliable for me. But using several controls and a geometric mean is also a good idea!
Indeed, Céline is very right, using reference genes belonging to different pathways is the best option. For example if you think the 18S is increasing in your treatment, anything related to mRNA translation will not help, since it will probably be proportionally increased (ribosomal proteins, translation initiation or elongation factors...). If U6 is also increased it means the splice pathway is increased, therefore one would expect transcription to be upregulated, so probably also the TBP or similar reference genes will not be very helpful. You can therefore try structural genes or metabolic ones... although in your case the situation seems difficult since when you increase transcription and translation pathways you will also increase metabolism and easily have hypertrophy which will need more structural proteins.
Maybe here gamma-tubulin could help, normally all cells have only one centrosome, unless they are dividing, so if mitosis is not strongly affected your g-tubulin levels should be pretty constant independent of the size of the cell and its metabolism. But I would not test it alone, possibly pair it to another reference on the metabolic side: again I would suggest an emergency gene, LDH (lactose dehydrogenase), instead of GADPH. There is much less in the cell and it is upregulated in hypoxia situations, which possibly will not be your case (at least if your work with cultured cells).
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