Ribodepletion: RiboZero kit (smaller rxns?)

[sjeschonek]

We are planning an RNA-seq experiment requiring rRNA depletion (in Xenopus laevis). Previous literature has shown success with our system using the Illumina RiboZero rRNA depletion kit...but it is fairly expensive.

Does anyone have experience using smaller reactions to increase the lifespan of the kit? I've heard that others have stretched the Illumina library prep kits by reducing reaction sizes...

Alternatively, is there any preference for alternative ribodepletion kits?

We were considering putting the ribodepleted RNA into the Kapa HyperPrep Library Prep Kit.

[nucacidhunter]

I would recommend looking at RiboCop. It is possible to scale down the depletion reactions in proportion to input quantity. They are offering free trial kits as well:

https://www.lexogen.com/ribocop-rrna-depletion-kit/

[sjeschonek]

Thanks for the recommendation. We just ordered a trial kit.

Do you have experience with the Lexogen library prep kit? Would you recommend it?

[nucacidhunter]

Lexogen QuantSeq 3’ mRNA-Seq is a cost effective method for DGE analysis and it works fine. Their whole transcriptome kits does not involve a standard fragmentation step. I am not sure if that would have any impact on final results compared to the current standard chemical RNA fragmentation based methods. They are offering free trial kits.