Best exome library when also sequencing small RNA?

[ejspina]

Hello,
We're interested in sequencing a small RNA library and an exome library from the same samples. The question arises, which method would be best for preparing the exome library (poly(A) selection or rRNA removal)?

Any personal opinions or experience is appreciated!

Thanks much,
EJS

[Bukowski]

Exome libraries are generated from gDNA not RNA.

If you are sequencing small RNA and polyA+ RNA (or ribosomal depleted RNA) then most likely they will be completely separate library preparations. I don't know of an all in one method.

Your decision on polyA+ or ribozero depends entirely on what the point of your investigation is. I recommend polyA for those who are simply interested in gene expression - who would normally have been happy with a microarray, and don't care about ncRNA, and ribosomal RNA depletion for those who are interested in ncRNA as a specific endpoint. With ribosomal RNA depletion options you will generally want to sequence more reads/sample than with polyA. For most people this ends up being a question of cost.

[ejspina]

Thanks for the response, your explanation is clear and confirms my reductionist interpretation of the two library preparation methods. Also, apologies for the confusion I'm not familiar with the lingo. So, what would be a good umbrella term to describe either polyA+ or ribominus RNA?

[Bukowski]

Thanks for the response, your explanation is clear and confirms my reductionist interpretation of the two library preparation methods. Also, apologies for the confusion I'm not familiar with the lingo. So, what would be a good umbrella term to describe either polyA+ or ribominus RNA?

I'd just refer to it as RNA-Seq (as opposed to, for example, small RNA-Seq)