qPCR plate setup - too many samples for one plate, how to divide samples? (Nov/04/2008 )

I am new to qPCR and have a question about the best way to setup my PCR plates. I have 35 samples that need to be done in duplicate (total 70 wells) and I am using 3 primer sets, so they will not all fit on one 96-well plate. Is it better to divide the samples by primer set (18S on one plate, gene 1 on a separate plate, gene 2 on a third plate) or is important to have all the genes for one sample on the same plate?

thanks...

It's more important to have all the samples for a gene on one plate. There may be little variability between runs but that will not matter if you have your calibrator and all other samples on same plate. If you'll sometimes have too many samples that won't even fit to single plate, add calibrator again to the next plate.

Also there is an option to run one plate with all samples and genes only single-well and then do this again to have a duplicate, but in your number of samples this won't help you now.