When comparing gene expression levels between two tissue samples, differences may arose for transcripts that pertain to cell subpopulations which are not in the same proportion in each of the compared samples. For instance, I am harvesting mouse olfactory epithelia. I will always get a diffrent proportion of cartilaginous tissue, mature and immature olfactory sensory neurons (mOSNs). Thus, when analysing RNASeq, differentail expresison analyses of mOSN transcript levels are affected by the quality of my dissection, and the biological differences between the mice. In qPCR, it is common to use normalization genes, ie. genes which expression pertain to the same cell type of the genes of interest, but which are not affected by the experimental condition. Did you already face the same problem? How would you normalize transcripts levels prior to differential expression analysis by DESeq or sleuth for instance?
Thank you in advance for any suggestion,