Selecting a proper reference gene(s) for RT-qPCR is an ongoing struggle.
It's easy to "do it", but it's significantly more difficult to do it right.
I will dedicate this topic to general discussion about selecting reference (sometimes called housekeeping) genes, software/application used and so on.
A web page first.
Massively resourced but rather ugly pages concerning normalization and reference genes selection on Gene-Quantification.info site.
(often contains fulltexts of papers)
The need for transparency and good practices in the qPCR literature - Nature Methods 2013
Evidence Based Selection of Housekeeping Genes - PloS ONE 2007
and of course
Today I came accross a free web tool to select reference genes using algorithms from four currently used applications geNorm, Normfinder, BestKeeper, and the comparative ddCt method.
Since I have used only one of them and this requires to only copy Ct directly from the Excel table (!!) it's like a huge help to refgene selection (I used GeNorm for some time, I wouldn't really call it user friendly..)
But since I can't compare with the others I don't have any comments on this would be appreciated.
(I may add later some sites/papers/... I found highly relevant, post any sources regarding the topic, if you want, too)