(while using "Nanodrop") for quantification of cDNA, one should quantify it as double-stranded DNA or single-stranded DNA?? I am using Fermentas kit for first standsynthesis of cDNA from total RNA and m not using RNaseH to degrade the RNA
ssDNA has higher optical density than dsDNA or ssRNA. See Wikipedia on Nucleic_acid_quantitation. DNA and RNA have different 260/280 absorption ratios. You could try averaging the values for DNA and RNA, but I doubt it would work.
To my knowledge, I came to know that the kit providing company suggest to use a part of your cDNA (some 5ul ) from your eluate. I tried to quantify as a ds DNA and I got huge amount as quantity but it doesnt help to synthesise my GOI. Only later I got to know this trick from my colleague and of course the company manual is saying this!
But UV analysis is not able to discriminate between RNA and DNA (ss or ds). You may want to use DNA-specific quantification by fluorimetry if RNA is abundant.