RiboPOOLs
Ribosomal RNA Depletion Kits
Any species
Choose from over 70 species-specific riboPOOLs or request a custom design
Enzyme-free protocol
No RNase H, no enzymatic steps - limiting risks of sample degradation
Unmatched flexibility
Combine probes for multi organism samples (e.g. host-microbiome)
The Concept
RiboPOOLs are hybridization-based ribosomal RNA (rRNA) depletion reagents designed for efficient rRNA removal. They consist of complex pools of biotinylated DNA probes that specifically bind to rRNA sequences.
During the process, these probes hybridize to their target rRNAs in total RNA samples. As a result, they form stable probe–rRNA complexes. Next, streptavidin-coated magnetic beads capture these complexes through a strong biotin–streptavidin interaction. This step enables fast and efficient separation. After magnetic removal, the rRNA-bound probes are discarded from the sample.
In the final clean-up step, remaining probes and reaction components are removed. As a result, you obtain high-quality rRNA-depleted RNA ready for downstream applications such as RNA-Seq and transcriptome analysis.
Find Your riboPOOL
Step-by-Step Guide
Select application:
Showcasing riboPOOL variants
Single Species riboPOOL
This version is designed to efficiently remove rRNA from samples of a single target organism, either from intact or intact & degraded RNA samples.
Pan-riboPOOLs
Pan-riboPOOLs represent a versatile, single-step solution for rRNA depletion across different phylogenetic groups. Unlike Single-Species riboPOOLs, designed to target rRNAs of specific organisms, the use of Pan-riboPOOLs is recommended whenever rRNAs from multiple species must be simultaneously depleted.
Combination riboPOOLs
Combination riboPOOLs are recommended anytime there is a need to deplete rRNAs originating from multiple and taxonomically distant species.
Custom Design
If you need ribodepletion probes for a species or RNA type not yet in our portfolio, we offer a Custom Design Service. This service provides a riboPOOL tailored to your specific experimental needs.
Ribo-Seq riboPOOLs
riboPOOLs optimized for ribosome profiling (Ribo-Seq) enable efficient removal of rRNA present in ribosome protected fragments (RPFs). Find out more here.
The Basics of ribosomal RNA depletion
What Is Ribosomal RNA (rRNA) Depletion?
Ribosomal RNA (rRNA) depletion removes ribosomal RNA from total RNA samples to enrich mRNA and non-coding RNA. Unlike poly(A) enrichment, rRNA depletion kits retain a broader range of RNA, including non-polyadenylated transcripts.
By reducing rRNA, this process improves RNA-Seq read quality and sequencing efficiency. As a result, more reads cover biologically relevant transcripts. Whether you work with model organisms or environmental samples, rRNA removal increases data depth and supports better discoveries.
With riboPOOLs, researchers can achieve:
- Up to 95% rRNA reduction
- Improved transcript detection and sequencing efficiency
- Reduced costs through lower sequencing depth
Why riboPOOLs?
Our rRNA depletion kits differ from conventional solutions by combining high target specificity with simple handling. Instead of enzyme-based methods, riboPOOLs use hybridization-based capture with biotinylated DNA probes. As a result, they enable efficient and selective rRNA removal while preserving RNA integrity.
Key advantages for RNA-Seq and transcriptomics:
- Enzyme-free workflow: No RNase H or complex steps, which reduces the risk of RNA degradation and sample loss
- High flexibility: Choose from over 50 species-specific kits or request a custom riboPOOL
- Multiplexing capability: Combine probe sets for multi-species samples, such as host–microbiome studies
- Broad RNA compatibility: Works with intact, fragmented, and FFPE RNA samples
- Proven performance: Validated in peer-reviewed Ribo-Seq and transcriptomics studies
Should I use poly(A) selection or rRNA depletion?
Not sure whether to use poly(A) selection or rRNA depletion? The tables below provide an overview of the most effective strategy depending on your sample type and downstream application.
Which organism do you work with?
| Taxon | Poly-A Selection | Ribodepletion |
|---|---|---|
| Bacteria | No | Yes |
| Archaea | No | Yes |
| Eukaryotes | Yes | Yes |
What downstream application do you plan?
| Application | Poly-A Selection | Ribodepletion |
|---|---|---|
| Short read sequencing | Yes | Yes |
| Long read sequencing | Yes | Yes |
| Direct RNA sequencing | Yes | Yes |
| Ribo-Seq | No | Yes |
What Is the Quality of Your RNA? Is your RNA intact or degraded?
| RNA Quality | Poly-A Selection | Ribodepletion |
|---|---|---|
| Intact (RIN > 8) | Yes | Yes |
| Partially degraded (6 < RIN < 8) | No | Yes |
| Degraded (RIN < 6) | No | Yes |
What sequences are you interested in?
| RNA | Poly-A Selection | Ribodepletion |
|---|---|---|
| Polyadenylated mRNAs | Yes | Yes |
| Long non-coding RNAs | No | Yes |
| Non-polyadenylated mRNAs | No | Yes |
In general, rRNA depletion offers greater flexibility—especially for degraded RNA, non-model organisms, or when studying non-polyadenylated transcripts.
Still unsure which kit suits your needs? Contact us for a recommendation.
Formats & Compatability
Publications
Using riboPOOLs
FAQ: Questions around our Ribodepletion Kit
How do riboPOOLs differ from existing ribosomal RNA (rRNA) depletion solutions?
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.
For my particular species, a Pan-riboPOOL and single-species riboPOOL are available. Which one gives better rRNA depletion?
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.
How long does a riboPOOL delivery take?
In stock riboPOOLs will be ready for delivery within ~1-2 days. Estimated delivery time will be ~1-2 weeks depending on your country. Custom riboPOOLs, depending on design complexity, require 3-4 weeks to be delivered.
My sample contains human and bacterial rRNA, can I combine riboPOOLs to use in a single depletion step?
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 sample and use a corresponding amount of riboPOOL. If this 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 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.
Which RNA-Seq library preparation kits are compatible with riboPOOLs?
riboPOOLs are compatible with most library preparation kits. However, the best compatibility is guaranteed for our own ARGO Library Preparation Kit.
My studied species is closely related to a species for which there is an existing riboPOOL. Would this riboPOOL work for my species too?
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.