Hi James, 

I have not done qPCR on 18S RNA, but I have used housekeeping gene 16S for one of my previous projects related to pathogen detection. 

The starting cycle would depends on your template concentration. Higher template would result in lower CT (earlier exponential phase). Having said that, the delta CT (CT gene of interest - CT house keeping gene) should be relatively constant independent of your template concentration (I am assuming your housekeeping gene is part of your template's strands and all samples are under equal treatments).

Hi James, 

18S RNA consider to be a very stable HK gene, however, its abundance its a common problem cause you have to be sure that after DNase treatment you have withdraw all the DNA content, other else you will have wrong positive results in HK expression in your samples. 

in my opinion, you should search for another HK, cause you have the opportunity to find a easier solution.

Hi dear James

I agree with Alexandros Mavrommatis.