I'm about to do a quantitative real time PCR on zebrafish and I'm unclear as to whether I should isolate RNA and then reverse transcribe to cDNA or just isolate DNA. What are the differences, advantages, disadvantages? How should I decide?
This depends on what you are investigating. If you want to study the expression of genes, then you need to extract RNA and make cDNA from it before analysis with qPCR. On the other hand, if all you are trying to determine is the copy number of a given gene in the genome, then purifying DNA is all you need to do.