mRNA-seq illumina GAII - microRNAs?

[vebaev]

Hi,
I have a question about finding pre-miRNAs precursor sequences among dataset from mRNA-seq? Is it possible since it is polyA method or the protocol preparation is somehow filtering only protein-coding long transcripts and it is highly unlikly to find miRNA precursors/transcripts among mRNA-seq data?

Thanks

[NicoBxl]

up

same question but with a TruSeq small RNA library kit and 36nt long reads.

[brooksma]

We definitely see pre-miRNA in our RNA-seq data sets. We use the TruSeq RNA kit which of course does a polyA pull down. We align to RefSeq and there are about 760 mirs in the mouse database. They are denoted with NR_xxxxxxx IDs. With the small RNA library prep I don't see them because I do a small RNA isolation step prior to library production which will get rid of the pre-mirs. I would assume that if you generated small RNA libraries on total RNA then you might get them based on which peaks you end up recovering after library amplification.

[NicoBxl]

Thanks brooksma,

Do you know some papers talking about RNA-seq and pri-miRNA detection ?