This is the first time I bring up a question. Your ideas will be greatly appreciated.
I am working on mRNA differential changes in the eye under different treatments. At the very beginning we used GAPDH as the housekeeping gene, and it looks OK for several treatments. However, when I use some new treatments, the GAPDH shows some regulation. In summary, I have 8 treatments/groups altogether, each treatment/group has several animals, in each individual animal there is a treated eye and a fellow control eye. In 6 out of 8 treatments, the GAPDH acts as a good housekeeping gene. In the other 2 treatmens, GAPDH got regulated in some of the animals, which means GAPDH is not good reference gene in these two treatments. The only way to solve the problem may be using a new stable reference gene for these two groups. So my question is, concerning publishing these data in the future, is it OK to use two different reference genes in the same paper, like use GAPDH for these 6 treatments, and use another reference gene for some other treatments. Since we are only doing comparison within the same treatment, compare the treated with the fellow comtrol sample under the same treament, not comparing between different treatments. Did any people see a paper using different reference gene like this?
Thanks a lot.
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