Here is the thing. I am using a method, called TU-Tagging, to isolate cell type specific RNA. You can find more about the method here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783170/
To explain it very briefly, there is an enzyme called UPRT (Uracil Phosphoribosyltransferase) which is expressed in Toxoplasma gondii. Under normal circumstances UPRT creates UMP from host cells' uracil and this UMP incorporated in RNA. However, they found that this enzyme cannot distinguish uracil and uracil analog 4-Thiouracil (Basically has thio on 4th position of the uracil). So, when 4-TU provided externally, UPRT incorporates 4-TU into RNA and you get thio-RNA. Then with basic biotinylation and streptaividin isolation you can get thio-RNA from your total RNA isolate. (Of course UPRT should be put to specific cell types of your interest)
Anyway, after the explanation (maybe it was unnecessary though) here is my question.
After I isolate my so called specific RNA, I check the purity by qPCR by using cell type specific markers. I do not have a reference gene. The only thing I am interested in is the presence or absence of markers (and also the fold change of course). Now, I have some data but I do not know how to present them (There is nobody in my lab experienced with qPCR and my experience is just so limited).
Do you have an idea how I can overcome this issue? I looked into some calculations but most of them are needed for reference genes or some other stuff. The only thing that I have is cycle numbers and my primers' efficiency. Do you think I can do something with these inputs? (I know that cycle numbers mean nothing in a plot, so I do not want to put cycle numbers basically.)
Thank you for reading it. Any help/idea would be very appreciated. I am so desperate. Thank you.