Poor quality bacterial RNA, need help!

[Arvind Bhagwat]

Dear Friends, I am stuck on step '0' on my bacterial RNAseq project, i.e. poor quality RNA.
My Experion runs look like this (see attached file).

I am using, ~10^8 cells, in 1.5 ml QiagenRNA Protect reagent, then use Qia RNeasy protocol with on column DNase. I get 4.8 ug total RNA yield.

Will appreciate any help/ suggestions you can provide.

[kerplunk412]

That doesn't look like degraded RNA to me, in fact without the extra peak it looks pretty darn good. Do you know what total RNA from your species should look like? I don't have experience with the Experion system, but on a Bioanalyzer if you run yeast RNA with a "eukaryotic total RNA" program it will tell you that even nice RNA is poor quality, because it doesn't see the peaks where it expects them. Because of course, yeast aren't eukaryotes...

[QSU88]

That's typical run profile for some bacteria RNA,You can also look at the gel ( from bioanalyer run) ,plus ratio of Ribo-RNA as reference to make final assessment.This sample looked good to me. Is this a cultured pure bacteria, or sample from patient with bacteria infection? Did you denatured RNA at 65C before run?