I am working on FFPE blocks. I need to find the genomic DNA contamination using picogreen. I usually use qRT-PCR using RNA as a template to find the genomic DNA contamination.
The standard control for DNA contamination in RNA samples in order to carry out qRT-PCR is to simply leave out the RT step (assuming you are using a kit with separate RT and amplification steps). DNA will amplify in this reaction, but RNA will not.
As Prescott indicates, you can always perform qPCR in parallel with a sample that never received the RT enzyme. If you have primers designed to amplify genomic DNA (e.g. qRT-PCR primers in the same exon) then you will see where genomic DNA is present. If your goal is to just perform good qRT-PCR not influenced by genomic DNA, then you can design primers to flank large introns....and of course run the no RT control to be sure your signal is RNA-dependent. Alternatively, there are kits to quantify dsDNA or ssDNA that are highly selective for DNA over RNA, like the iQuant kits.
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