Hi,

You can not obtain the same results from Nanodrop and Qubit because of different principles of measurement.

Trust to Qubit and Tapestation. 

Hi,

I agree with Marcela, although I've never had such differences the greatest I got were around 2 fold less amount by Qubit. 

This is an old question but for the sake of people searching for this answer, here is the reason:

Nanodrop is just a UV spec reading. It is only looking at absorbance at 260 nm. Plenty of things absorb at 260 nm other than the RNA you make in your IVT reaction. This includes the T7 protein, pyrophosphatase (if you use it), your DNA template, the NTP monomers, the abortives, truncates, and even salt. Your nandrop is giving a signal for ALL of these things.

Qubit is better. It gives a reading based upon an intercalator that is specific for RNA. This means that it will (likely) only give signal for your full length RNA, abortives (above a certain length), and truncates.

This explains the disparity between your nanodrop and Qubit readings. And btw, a reading of 4000 ng/uL on the nanodrop is too high to trust. 10 fold dilute that and try again.

Still, 10x is a big difference and likely means that your IVT yield was very low.

Better than Qubit would be to actually purify your RNA (DNase followed by EtOH precip/dT/etc., ultrafilter, recover) and then run the final material on a gel or capillary electrophoresis or HPLC and then compare against a standard curve.

Pain in the ass, but it's the best way.