The people i sent my samples to for DNA isolation also measured the DNA concentration for me via a nanodrop.
To my frustration there is massive variation in the "quality" or suitability of the extracted DNA for PCR as assessed via the use of a pair of primers which i use as a positive control obtained from the jackson lab which they use for their PCR experiments on genotyping mice. For the quality checks i used 250ng of DNA with a primer concentration of 0.5um and preformed 40 cycles. In some samples i get a very strong band while in others i get either very faint bands or no bands at all. The PCR kit i use is the roche fast start pcr master catalogue number 04710444001.
What i am intersted to hear about is do people have any comments on the DNA extraction protocol which was used and do most of ye who do genotyping experiments use commercial kits to purify your DNA which you will use for PCR experiments if so are there any ones you reccomend.
Thirdly have any of ye tested different PCR kits with the same DNA template and found any differences between manufacturers in their ability to produce a succesful PCR over an alternative supplier?