FAQ

The riboPOOLs are a defined complex pool of biotinylated DNA probes designed with proprietary algorithms. Compared to other solutions, riboPOOLs are non-polyA-dependant, enzyme-free, highly efficient and can be used to deplete rRNA or other abundant RNA from single or multiple species.

riboPOOLs for single species perform the best, generally achieving > 95% rRNA depletion efficiency. Pan-riboPOOLs for multiple species were designed to achieve a balance of versatile application across various species and efficient depletion. Pan-riboPOOLs can also achieve high depletion efficiency but may vary between species. Please contact us to ask how your Pan-riboPOOL of choice performed for your species.

Ready-made riboPOOLs can be delivered within 1-2 weeks. Custom riboPOOLs, depending on design complexity, require 3-4 weeks to be delivered.

Standard RNA-Seq riboPOOLs perform best with DNA-free, high quality RNA of RIN values ≥ 7. With increasing RNA degradation, pulldown efficiency may be reduced; however the high complexity of riboPOOLs helps to counter this. Additionally, a specific FFPE/degraded RNA riboPOOL may be available for your species.

Yes. riboPOOLs can either be combined by the user or a Combination riboPOOL can be purchased from siTOOLs Biotech. To combine riboPOOLs, determine the ratio of species-specific RNA present in the sample and use a corresponding amount of riboPOOL. If this is not known, use a 1:1 ratio and optimize accordingly. Up to four riboPOOLs may be combined in a Combination riboPOOL at ratios specified by the user. When combining riboPOOLs, keep the total probe amount to 100 pmol/reaction and ensure proportion of hybridization buffer is kept constant i.e. 5 μl in 20 μl final volume.

riboPOOLs perform well for input amounts down to 10 ng. For input amounts < 10 ng we recommend reducing the riboPOOL probe amount to ~30 pmol per reaction. To do this, resuspend the riboPOOL with 3X the recommended volume of nuclease-free water and use 1 μl of the resulting solution per reaction.

Similar to traditional RNA-Seq, the predominant fraction of Ribo-Seq samples often comprises ribosomal RNA (rRNA), with RPFs (desirable reads) typically representing less than 5% of the sequenced reads.
Our Ribo-Seq riboPOOLs are specifically designed to deplete rRNAs from Ribo-Seq samples and significantly increase RPFs reads mapping rates. Check out our Ribo-Seq riboPOOLs portfolio or request a custom design for your species of interest. 

riboPOOLs are compatible with most library preparation kits and have been used successfully with Stranded Total RNAseq by Illumina, KAPA RNA HyperPrep and NEBNext library prep kits.

Please contact us at info@sitools.de to check compatibility of the riboPOOL for your species.
We can always run an in-silico check for the coverage of our current riboPOOLs.