Question: How to know a RNA-seq is polyA or total-RNA-seq in GEO?
2
gravatar for bxia
3.4 years ago by
bxia150
bxia150 wrote:

How to know a RNA-seq is polyA or total-RNA-seq in GEO?

Does GEO require that kind of meta data during submission?

Thanks,

rna-seq geo • 1.9k views
ADD COMMENTlink modified 3.4 years ago by Devon Ryan97k • written 3.4 years ago by bxia150
5
gravatar for Devon Ryan
3.4 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

As a rule of thumb, if a project doesn't explicitly mention looking at total RNA then the odds are high that it's polyA selected. When in doubt, you can always align against rRNA, since the alignment rate for polyA selected samples will be very low (<<1%), while rRNA-depleted (aka "total RNA") will have >1% rRNA (sometimes up to ~30%).

ADD COMMENTlink written 3.4 years ago by Devon Ryan97k

So there is no way to figure them out without mapping result, right?

ADD REPLYlink written 3.4 years ago by bxia150
1

Note that even alignment is not guaranteed to distinguish the two. Our core has sequenced plenty of polyA-selected libraries that contain substantial amounts of rRNA (some people are better at library prep than others).

ADD REPLYlink written 3.4 years ago by harold.smith.tarheel4.6k
1

Wow, I haven't seen any polyA samples over 0.1% or so rRNA come through our core. Of course I've seen rRNA-depleted samples with 30-40% rRNA, so perhaps we're trading off high polyA quality for low rRNA quality :P

ADD REPLYlink written 3.4 years ago by Devon Ryan97k

Our core takes a laissez-faire approach to library prep - we offer as much guidance as the user is willing to accept, but ultimately it's the user's responsibility to make good libraries (or not). If the libraries pass basic QC (PicoGreen quantification, plus Bioanalyzer for adapter dimers), they get sequenced. We've had a few that were >90% rRNA/multi-mappers (essentially total RNA).

ADD REPLYlink written 3.4 years ago by harold.smith.tarheel4.6k

That or trying to discern from the methods what they did.

ADD REPLYlink written 3.4 years ago by Devon Ryan97k
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