riboPOOLs - ribosomal RNA Depletion Kits
High-performance rRNA depletion kits that remove unwanted ribosomal RNA from total RNA samples, enabling clearer insights for applications like RNA-Seq and Ribosome Profiling.
Any species
Choose from over 70 species-specific riboPOOLs or request a custom design
Enzyme-free protocol
No RNase H, no complex enzymatic steps - limiting risks of sample degradation
Unmatched flexibility
Combine probes for multi organism samples (e.g. host-microbiome)
Wide spectrum of RNA quality
Works effectively with intact and degraded RNA
Selecting the right riboPOOL
Pan-riboPOOLs
Designed to efficiently remove rRNA from any species within their target group. By targeting conserved regions of rRNA, they are ideal for samples containing RNA from multiple or unknown related species (e.g., microbiome samples).
Pan-riboPOOLs also help optimize reagent usage in research projects that involve several different species.
Combination riboPOOLs
Many sample types contain total RNA from multiple, often distantly related species. A common example is infected tissue, where host RNA - such as from an animal or plant - coexists with pathogen RNA. Combination riboPOOLs allow to combine up to four probe sets to deplete rRNA from different species simultaneously, while keeping costs optimized.
Custom Design
Whether you need ribodepletion probes for a species not yet included in our portfolio or you want to remove additional RNA targets from your samples, our Custom riboPOOL Design Service provides a ribodepletion kit tailored to your experimental needs.
Ribo-Seq riboPOOLs
These probes cover the entire ribosomal RNA sequence, thereby ensuring that any potential contaminant sequence is effectively targeted by a corresponding riboPOOL probe. Abundance of each riboPOOL probe has also been optimized, with probes that target known abundant contaminants being present at higher concentrations.
Single Species riboPOOL
Designed to efficiently remove rRNA from samples of a single target species. Most Single Species riboPOOLs are optimized for high-quality RNA (riboPOOLs for intact RNA), but for some species we also offer versions suitable for both intact and degraded RNA (riboPOOLs for intact and degraded RNA). Probe sets for intact RNA are designed to provide efficient ribodepletion while minimizing off-target effects and probe carryover. When the input RNA is degraded, more probes are required to ensure that every rRNA fragment is captured. In these cases, we slightly relax our probe-selection parameters to increase coverage generated by our design workflow.
Single-Species riboPOOLs
Specifically designed to deplete rRNAs in single species
Human-Mouse-Rat riboPOOLs
Single solution for rRNA depletion in human, mouse and rat models
Pan-riboPOOLs
A single-step rRNA depletion for multiple species
Ribosome Profiling
Optimized for rRNA depletion in ribosome profiling preparations
Combination riboPOOLs
Combine up to 4 riboPOOLs to deplete rRNA in different species
Custom riboPOOLs
Not finding what you are looking for? Order a custom riboPOOL
What is Ribosomal RNA (rRNA) Depletion and Why Does it Matter?
rRNA depletion is the process of selectively removing ribosomal RNA from total RNA samples to enrich for messenger RNAs (mRNAs) and non-coding RNAs. Unlike poly(A) enrichment, rRNA depletion kits retain a broader RNA population, including non-polyadenylated transcripts.
rRNA depletion enhances read quality and efficiency by increasing the proportion of biologically informative transcripts. Whether you're working with model organisms or environmental samples, removing rRNA ensures greater data depth and discovery potential.
Using riboPOOLs, researchers can achieve:
- 95% reduction of rRNA content
- Improved transcript detection and sequencing efficiency
- Cost savings from reduced sequencing depth
Why riboPOOLs are the preferred rRNA Depletion Kit
riboPOOLs stand out from conventional rRNA depletion kits by combining high target specificity with exceptional ease of use. Instead of enzyme-based protocols, riboPOOLs use hybridization-based capture with biotinylated DNA probes, ensuring efficient rRNA removal without compromising RNA integrity.
- Enzyme-free protocol: No RNase H, no complex enzymatic steps—fewer risks of sample degradation
- Unmatched flexibility: Choose from over 50 species-specific riboPOOLs or request a custom mix
- Multiplexing ready: Combine probes for multi-organism samples (e.g. host-microbiome)
- Resilient to RNA quality: Works effectively with intact, fragmented, or FFPE RNA
- Scientifically validated: Proven performance in peer-reviewed Ribo-Seq and transcriptomic studies
Which rRNA Depletion Method is Best for Your Experiment?
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.
How riboPOOLs Work
- Hybridization: Biotinylated riboPOOL probes bind specifically to target rRNAs.
- Capture: The probe–rRNA complexes are pulled down using streptavidin-coated magnetic beads.
- Purification: The RNA sample is purified to remove rRNA, leaving behind valuable transcripts.
The riboPOOL workflow is simple to implement in most RNA workflows and works with degraded RNA (FFPE), low input (10 ng), and complex samples. Protocols are available for ethanol precipitation or magnetic bead cleanup.
riboPOOL Ribodepletion Kits: Formats & Compatibility
Our riboPOOL kits provide an all-in-one solution for efficient ribosomal RNA (rRNA) depletion across a wide range of species. Designed for both research and clinical applications, the kits are available in multiple formats to suit your input and throughput needs.
- Available formats: Trial (6 reactions), Standard (12, 24, or 96 reactions)
- RNA input range: 10 ng – 3 µg total RNA
- Applications: Ribosome profiling (Ribo-Seq), transcriptomics, degraded RNA, FFPE samples
- Includes: Biotinylated riboPOOL probes, hybridization buffer, magnetic bead protocol
- Depletion targets: rRNA, optional tRNA co-depletion kits available
- Workflow compatibility: Validated with major RNA-Seq and Ribo-Seq library prep kits (e.g., NEBNext, Zymo, Illumina)
All riboPOOL kits are shipped lyophilized and come with detailed protocols. Need a specific organism? Browse our riboPOOLs by species or request a custom depletion kit.
Prefer to use your own hybridization buffers? riboPOOL probes are also available stand-alone, shipped lyophilized with nuclease-free water. Buffer recipes can be found in our Resources section.
FAQ: Using riboPOOLs for rRNA and Ribosome Profiling
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.
Can riboPOOLs be used with degraded RNA?
Standard RNA-Seq riboPOOLs perform best with DNA-free high quality RNA of RIN values ≥ 7. With increasing degradation of RNA, 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.
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.
My sample has < 100 ng of RNA, can I still use riboPOOLs?
riboPOOLs perfom well for input amounts down to 10 ng. For Input amounts < 10 ng we do recommend to reduce 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 resulting solution per reaction.
Can riboPOOLs be used for ribosome profiling samples?
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 significanlty increase RPFs reads mapping rates. Check out our Ribo-Seq riboPOOLs portolio or request a custom design for your species of interest.
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.