Removing rRNA from RNA-Seq

[SeeElle]

Hello-

Let me know if this has already been discussed...

I have a lot of rRNA contamination in my RNA-IP samples for seq based on an Agilent RNA profile. I don't expect my protein complex to bind to rRNAs. I've heard of doing a ribosomal reduction, but I've also heard a low success rate for them.

Has anyone been able to overcome this difficulty?

Has anyone proceeded despite abundant rRNA contamination? Was the data usable despite most of the coverage being occupied by rRNAs?

Has anyone used the Epicentre or Invitrogen's ribosomal reduction kit on c.elegans?

[wangleibio]

you can use Poly(A)Purist™ Kit(AM1916)　ｋｉｔ。

[SeeElle]

Thanks wangleibio. However, I do not want to polyA select because some of my target RNA can be short or unpolyadenylated RNAs.

[NextGenSeq]

I've used RiboZero for human and mouse RNA and it worked well. One caveat is that if you are using cultured cells and have mycoplasma contamination, the mycoplasma RNA will show up in your RNA-Seq library.