I measured the concentration of my RNA with nanodrop and they seems to have a really high concentration, but when I sent them to Bioanalyzer, it could not detect some samples with nanochip. For exemple, one of my samples had 312.3 ng/µl at nanodrop, but when I ran the bioanalyzer, it gave me a concentration of 10 ng/µl and did not gave me the RIN. So I tried again with Picochip and I could get the RIN (8.2) but the concentration was 2.300 pg/µl. Now I don`t know in what method I should trust to run my PCR because the difference in concentration is too high. Can someone help me with that?
I have been using nanodrops for some time and never used other machine to measure the nuclei acid concentration. So far nanodrops always give me consistent and good results. When my samples were sent for outsource sequencing, no problem arised as well. It means nanodrops reading is consistent.
Nanodrop measures A260, whereas Bioanalyzer measures fluorescence of an intercalating dye. Is the spectrum yielded by the Nanodrop comptible with nucleic acids ? Also, fluorescence detection with intercalating dyes is far more sensitive with ds nucleic acids (DNA) than with ss nucleic acids (RNA). Is you Bioanalyzer properly calibrated ?
I don't know about calibration Pierre because I sent them to a facility, but I guess that if they do this all the time they should have it calibrated.
Mathew, I always used Nanodrop to test my RNA and was always pretty good. I know I should not use Bioanalyzer as a quantitative assay, but the thing is that the difference in concentration is too high (Bioanalyzer not even detected RNA that was supposed to have 312ng/µl) so that is why I thought it is wired. But as you said maybe I have DNA contamination, that is why I am getting this high concentration with nanodrop. It wasn't me who extracted RNA from those samples but I know that they used Trizol for that.
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