I understand the importance of choosing a good gene standard for normalization of qPCR values. Even so, I would like to know if it could be performed (unless it is not the best option) the normalization of the data using GAPDH in a case of mitochondrial disorder, given that probably the mitochondrial respiration is impaired and maybe the glycolisis is favoured in this case.
I guess that if you control in the experiments that the expression values obtained for GAPDH are the same in every cell line (mutant and control ones) you could use that gene for normalization and comparison between lines.
Thank you very much.
It could be a good idea to look at other housekeeping genes that are a little less associated with metabolism in your particular case, as like you said, maybe the mutant cells will have altered levels of gapdh; maybe run the gapdh for fun anyways.