I assume that the rather low 260/230 ration comes from residual guanidine thiocyanate which is one of the main components of the Trizol reagent you used. I think that your RNA preparation is still good enough for NGS because your other assays indicate a high quality of your preparation. In the document I attached you can find further information on the effect of GTC on RNA preparations. Up to 100 mM (which is rather high) GTC is tolerated by most downstream applications. I am interested what other RG members think.

Cheers, Christian 

Good question. My question is: what RNA NGS protocol are you going to sequence?

We used the Zymo-kit and it worked very well for most samples we had extracted. Later we included additional washing steps and didn't need a cleanup

dont look the nanodrop values trust your RIN number its good so go ahead

Thanks very much, all . I am gonna to use the Clontech stranded RNA lib prep kit to do the mRNA seq lib. I did the Agilent  screen tape test for checking the samples from  both non-clean up and clean-up by ZYMO. The RIN increased from 9.5-10. And the band looks more clear. I was thinking that might be the nice work got from ZYMO RNA clean kit.

I've had the same kind of experience with diverse types of RNA prep, mainly from columns, but it never give bad results in RNA-seq. As said, as long as your RINs are OK, libraries prep takes so many steps with different kinds of purification that the contamination will be taken away. Of course it's always better to have the cleanest as possible samples, but I would not worry too much about low A260/A230 ratios.