The first thing that comes to mind is to represent mRNA expression levels as FOLD-CHANGE from baseline in each species.

Treatments are bound to change small or large changes (up regulation or down regulation, or none) and thus expressing your results and 100% change or fold change would be an appropriate way to plot your results. I'm curious of other suggestions.

This topic is very interesting. I am looking forward to expertise suggestion. I have one idea but confusing, that you can make a common primer sequence for both species. I am waiting for an appropriate response.

Hello Laurence Stuart Dawkins-Hall

Thank you very much for your answer. I'm going to explain you in detail what I have planned to do to be able to use the comparative Ct method, in case you can give me your opinion. First of all I have verified that both the chick study gene (e. g. GAP43) and the chick housekeeping gene (e. g. GAPDH) are not amplified when I study a cell culture with only rat Schwann cells. Once this is known, I will use these chick genes to study chick DRG in co-culture with rat Schwann cells. Thus, it doesn't matter which part of the studied RNA is from rat and which part of RNA is from chick, since I normalize de PCR results with respect to the species of interest (the chick) using the chick housekeeping gene. Would this procedure be correct?

Thank you in advance!

Hello Fernando Gisbert Roca ,

assuming that your primers/probes are sufficiently specific (for the species and the gene of interest), I don't see any issues with your plan.

Since you seem only interested in transcriptional changes in chicken DRGs and don't plan to analyze rat transcripts, I would consider the co-culture with rat Schwann cells as kind of a (pre-)treatment. Hence, as long as you include proper control conditions (e.g. chicken DRGs +/- rat Schwann cells; rat Schwann cells only), you should be able to use comparative Ct here.

Best wishes