Question: Recognize rRNA remove protocol from gene expression profile
gravatar for Niek De Klein
2.2 years ago by
Niek De Klein2.4k
Niek De Klein2.4k wrote:

We have a large amount of samples for which we don't know the protocol that was used to extract the RNA. We want to know which samples were processed using the Poly-A selection protocol, and which with the Ribo-Zero-Seq protocol. Is there a tool available that can do this?

poly-a rna-seq ribozero • 623 views
ADD COMMENTlink modified 2.2 years ago by 5heikki7.0k • written 2.2 years ago by Niek De Klein2.4k

I think tRNAs are the most useful thing you can look at, since they would not be taken up by poly-A selection but they would not be removed by ribo-zero protocols.

ADD REPLYlink written 2.2 years ago by Martombo1.9k
gravatar for 5heikki
2.2 years ago by
5heikki7.0k wrote:
If it's a metagenomic sample and ribo zero was used, then if you screen the sample for SSU rRNA, you'll find that the relative abundance of archaeal and eukaryotics SSU rRNAs is very high in relation to bacterial SSU rRNAs.
ADD COMMENTlink written 2.2 years ago by 5heikki7.0k
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