We did SNP array with Agilent chip. But sometimes we would get noisy data. We tried a lot of methods to fix this but failed to do so. We are sure our DNA has no RNA or protein contamination or degradation. Only the DNA concentration is different between the Nanodrop and Qubit methods. Once the DNA concentration measured by the two methods is the same, we will get good data. I have already asked Agilent support, but they couldn't give me an answer.
Likely because Nanodrop has never been known to be very accurate in its DNA concentration measuring capabilities...it tends to overestimate DNA concentration especially if there are even trace amounts of organic solvents left behind from extraction. I don't know how Quibit is on this spectrum of methods that measure DNA concentration. You can always use something like PicoGreen to get accurate readings. All of the microarray centres that I have sent my samples to for SNP arrays or even WGS/WES use PicoGreen to measure the DNA concentration prior to running their pipeline.
Qubit is a machine developed by Invitrogen to measure the concentration of dsDNA with fluorescent dye just like Picogreen
You also have to consider the (actual) linear dynamic range of the instrument you are using. The NanoDrop is quite good at measuring DNA at high concentrations, but quite poor at lower concentrations. The Qubit, in my experience is better at the lower end, but very poor at really high concentrations.
There is another issue, however, that you should consider, and that is the integrity of the DNA sample. The Nanodrop measures ALL nucleotides, whether or not they are incorporated into DNA, whereas the Qubit will only measure intact DNA. You could also run the DNA on an Experion or Bioanalyser to evaluate the integrity.
I would give a look to the Trinean's instruments. They have this new technology which allows you to measure 96 samples in 6 minutes without any dyes, and still get Qubit accuracy.
It's quite new but still worth to try it.
Hi:all,
Thanks for your answers. Now I known what's problem with. Nanodrop measure all DNA (single strand and double strands) but, Qubit only measure double strand DNA depend the dye we use. so , If a DNA sample was denature by heating. so the concentration would be much different by two methods measurement.
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