Define quality! Integrity? Purity? Folding??

And what RNA do you analyse? Total? PolyA+? In vitro transcribed??

For purity (any kind of RNA), spectrophotometric methods are still the easiest (nanodrop being one of the common instruments).

For overall integrity of total RNA or single transcripts, Bioanalyzer is an industry standard (overpriced and underexplained. Even the engineers do not understand how RIN is calculated!), but really, a simple agarose gel will give you essentially  the same information: 28S/18S is close to 2? You're doing fine!

For accuracy of single transcript termini, run a denaturing urea gel and stain.

For folding, you have to run a non-denaturing gel and ensure single species.

So really, the question is what you want to measure and why...

Good luck!

From my expertise working with RNA, I might say Bio-analyzer is the best method to have a sense of the RNA quality. Is not necessary many sample (1ul is enough) and it gives you the RIN (RNA Integrity Number). For instance, with this information you know if your RNA is degraded or not.

I have used also another method called Qubit (from Invitrogen) but in my opinion, is not so accurate. 

Define quality! Integrity? Purity? Folding??

And what RNA do you analyse? Total? PolyA+? In vitro transcribed??

For purity (any kind of RNA), spectrophotometric methods are still the easiest (nanodrop being one of the common instruments).

For overall integrity of total RNA or single transcripts, Bioanalyzer is an industry standard (overpriced and underexplained. Even the engineers do not understand how RIN is calculated!), but really, a simple agarose gel will give you essentially  the same information: 28S/18S is close to 2? You're doing fine!

For accuracy of single transcript termini, run a denaturing urea gel and stain.

For folding, you have to run a non-denaturing gel and ensure single species.

So really, the question is what you want to measure and why...

Good luck!

Thanks for all help and answers.