I am doing qRT-PCR to check the expression of certain miRNA and mRNA in the mitochondrial fraction. But I am not able to determine which reference gene I should be taking in the case of the mitochondrial fraction. I have currently used U6 and 5S rRNA as reference genes to check the expression of miRNA, and it is showing variation. In the case of checking the expression of certain mRNA in the mitochondrial fraction, I am not able to understand the reference mRNA which I should use. Can anyone suggest any control which works best in the case of mitochondria?