mRNA-seq from Mirvana prep

[mbjohnson]

Hi all,
Has anyone used the large, presumably mRNA-enriched fraction from the Mirvana protocol for TruSeq library prep and Illumina mRNA-seq? Bioanalyzer tells me there's 0% ribosomal contamination in my large RNA fraction from the Mirvana prep, but I'm wondering if I should still do the poly-A selection beads step with the TruSeq kit or not.
Thanks for your input,
Matt

Edit: I just realized that the size range of these "mRNA" samples looks huge; see attached Bioanalyzer gel, left side samples. Perhaps a lot of unspliced pre-mRNAs? So I should probably still do poly-A selection...

[mikaelk]

I have not used the mirvana kit but there is one thing that I know for sure.
If you do not see any ribosomal peak, it does not mean that you don't have any rRNA. You might came down from 95% of rRNA to 5% but in terms of ratio you might then have a 50-50 with mRNA.
In my experience the only way to be sure that you have removed everything (as closely as possible) is to do qPCR.
I would go for a polyA step just in case.