To get good and reproducible results from a qPCR experiment, you must must start from same RNA concentration in your samples, otherwise you could have a biased differential gene expression. To check the RNA concentration I generally use Nanodrop but if I load an agarose gel based on that read concentration I don't have the same band intensity almost always, that's the Nanodrop measurements are not 100% reliable. For this reason I visually adjust the samples concentration comparing the band intensity on the agarose gel. This method can create bias as well, of course. How do you usually do?
Look, the nano drop will tell you the concentration of RNA molecules, but it won't tell you their quality. Degraded RNA and intact RNA will give the same nano drop readings. I usually run a gel to see if my RNA is intact, if yes, I use the nano drop to quantify, and then call it good enough to proceed.
Test gel is indeed important and should usually be the first thing to do. If you think your Nanodrop reading is not trusted I would suggest measuring multiple times and taking average and then normalize/adjust the concentration.
I agree with Katie A S Burnette running a gel is mostly to test the RNA integrity. The nanodrop should give pretty reliable readings that is what I have used in the past for quantification. If the numbers are very different then you could use a qubit to quantify if you want.
Gel electrophoresis gives and idea about the quality of your RNA. If its comes with nice two bands. yes its true. you didn't get the same intensity of bands because of different concentration. so measure with the nanodrop and get the RNA quantity. Normally I make the cDNA with 1ug/ul of final concentration. so in qPCR its not affected to the sample comparison.
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