Save truseq stranded mRNA polyA(-) supernatant for small RNAseq?

[Chinanicole]

Has anyone tried to save and sequence the polyA(-) supernatant from Illumina's TruSeq stranded mRNA library prep kit? If so, any advice or insight into things to consider using the supernatant - ie: would I do another phenol extraction or something to pellet out the polyA(-) RNA then suspend in H2O?

I'm interested in small RNAs (miRNA, piRNA) in particular so I assume I'd need to clean up the supernatant on a gel to size select for 20-30 nt or maybe use another rRNA depletion to clean up the samples.

Thanks!

This kit:

https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-stranded-mrna.html

[nucacidhunter]

It is a good idea to try. Simplest way would be to dilute the bead supernatant to reduce salts concentration coming from binding buffer and then use a Zymo RNA Clean & Concentrator column which gives options to purify the required size range including small RNA for follow up application.

[Chinanicole]

I have a bunch of Qiagen miRNeasy columns as well (> 20 nt) - any reason to use the Zymo over the Qiagen?

Thanks!

[nucacidhunter]

Zymo kit is designed for purification and elution volume can be as low as 5 ul. miRNeasy is for RNA extraction from tissue and cells and has to be modified for purification with risk of loosing material.