rRNA depletion for any species

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The world's most flexible rRNA depletion solution

riboPOOls' unique feature is their high complexity pooling approach based on our Pack Hunter design algorithm.
The high complexity of riboPOOLs ensures optimal and maximum rRNA coverage, allowing for efficient and cost-effective rRNA removal of any species or abundant RNA.
riboPOOLs are available for single species (e.g., Homo sapiens, Drosophila melanogaster, etc.) and multiple species.

Benefits of riboPOOLs

rRNA depletion for any species
High complexity probes for efficient, reliable rRNA removal

Wide RNA-input range (10 ng – 3 µg)
riboPOOLs for highly degraded samples (FFPE)
special solution for ribosome profiling


World Leading Scientist publish with riboPOOLs

Bioscience, Biotechnology, and Biochemistry
Mio Takeuchi, Hideyoshi Yoshioka (2021) Acetate excretion by a methanotroph, Methylocaldum marinum S8, under aerobic conditions

Nature Protocols
Y. Long (2021) FLEP-seq: simultaneous detection of RNA polymerase II position, splicing status, polyadenylation site and poly(A) tail length at genome-wide scale by single-molecule nascent RNA sequencing

Neil Fleck & Christoph Grundner (2021) A Cas12a-based CRISPR interference system for multigene regulation in mycobacteria

npj Biofilms and Microbiomes
J. Andersen et al. (2021) Identification of small molecules that interfere with c-di-GMP signaling and induce dispersal of Pseudomonas aeruginosa biofilms

Nature Communications
La Rosa et al. (2021) Compensatory evolution of Pseudomonas aeruginosa’s slow growth phenotype suggests mechanisms of adaptation in cystic fibrosis 12 3186


PLOS Genetics
Fuchs et al. (2021) Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach

BMC Genomics 
Kim, I et al. (2019) Efficient depletion of ribosomal RNA for RNA sequencing in planarians 20, 909


Ribosome profiling

Bhat et al. (2021) Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome

Nature Communications
Blaze et al. (2021) Neuronal Nsun2 deficiency produces tRNA epitranscriptomic alterations and proteomic shifts impacting synaptic signaling and behavior, 587, 14

Nat Protoc 
Galmozzi, C. V. et al. (2019) Selective ribosome profiling to study interactions of translating ribosomes in yeast 14, 2279–2317

Nature Communications
Ryan. D et al. (2020) A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gutmicrobe Bacteroides thetaiotaomicron (20) 11


Specific, efficient rRNA depletion with riboPOOLs

Human riboPOOL depleted 98.6% of rRNA, compared to 80.6% by Ribo-Zero


Mouse riboPOOL depleted 96.4% of rRNA, compared to 86.1% by Ribo-Zero



Reproducible results with riboPOOLs

High reproducibility between biological replicates with human riboPOOLs


High reproducibility between biological replicates with mouse riboPOOLs



rRNA depletion for your species


The Pan-riboPOOLs are a versatile rRNA depletion solution that allows for simple mono- and multitranscriptomic studies using a single-step rRNA depletion for a phylogenetic group (e.g., bacteria, fungi, or mammals).

The option to combine riboPOOLs facilitates single-step rRNA depletion in mixed samples such as environmental, blood, or infected tissue (e.g., SARS-CoV-2) samples. The so-called combination riboPOOLs enable simple metatranscriptomics studies by combining 2-4 riboPOOLs of non-related species.


Pan-Prokaryote riboPOOL (Bacteria and Archaea)
Pan-Bacteria riboPOOL
(Gram Positive and Gram negative Bacteria)
Pan-Archaea riboPOOL
Pan-Plant riboPOOL »
Pan-Bird riboPOOL
Pan-Mammal riboPOOL

Pan-Sponge riboPOOL
Pan-Fungi riboPOOL
Seawater riboPOOL
Blood Parasite riboPOOL

Single-Species riboPOOLs

Single-species riboPOOLs are available for well-studied and lesser-known species (Escherichia coli, Arabidopsis thaliana or Schmidtea mediterranea and many more). Single-species riboPOOLs are specifically designed based on the species' rRNA to target both conserved and non-conserved regions.

Moreover, single species riboPOOLs are used on high quality to medium quality RNA and result in high rRNA depletion efficiency.

Degraded RNA and Ribo-Seq RNA Degraded RNA (FFPE samples) or ribosome profiling RNA can be processed with our special applications riboPOOLs. (link to special applications)

Single Species riboPOOLs

Escherichia coli
Bacillus subtilis
Caulobacter crescentus
Clostridium perfringens
Stenotrophomonas sp.
Mycobacterium smegmatis

Haloferax volcanii

Oryza sativa
Arabidopsis thaliana

Mus musculus / R. norvegicus
Homo sapiens sapiens
Chinchilla lanigera
Gallus gallus domesticus

Amphimedon queenslandica

Saccharomyces cerevisiae
Pichia pastoris
Staphylococcus aureus
Ustilago maydis
Schizosaccharomyces pombe

Drosophila melanogaster
Plautia stali
Leptinotarsa decemlineata
Ixodes scapular
Aedes albopictus
Bombix mori

Danio rerio

Schmidtea mediterranea

Crassostrea gigas
Loripes orbiculatus and
Lucinoma aequizonata (Clamps)

Chlamydomonas reinhardtii
Emiliania huxleyi
human Globin mRNA


Need custom riboPOOL?

Is your species not listed here? Let us set up a custom riboPOOL.
Custom riboPOOLs include a one-time setup fee. You can purchase the custom riboPOOL as a ready-made riboPOOL at any kit or probe size.
Contact us for more information.


How do riboPOOLs work?


How the Pack Hunter Approach improves specificity and reliability of ribosomal RNA depletion with riboPOOLs

riboPOOLs are highly complex and defined oligo pools containing 60-350 distinct biotinylated DNA probes. riboPOOLs have significantly improved rRNA removal efficiency and result in robust and reproducible RNA-Seq libraries.

This is attributed to three key features:

Feature 1: High-complexity pooling
Increased diversity of riboPOOL probe sequences ensure maximum target coverage. Additionally, the low concentration of individual probes leads to higher specificity and efficiency.

Feature 2: Detailed Bioinformatics Design
We ensure maximum and optimal rRNA coverage, optimal binding to rRNA sequences, and avoidance of targeting similar genes.

Feature 3: Quality Production Process
We manufacture and maintain our riboPOOLs in accordance with strict Quality Management standards. HPLC is used to refine riboPOOLs to ensure the highest purity levels.

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Find the right riboPOOLs Kit & Probes

riboPOOL kits

riboPOOL probes

  • riboPOOLs and siBeads (streptavidin-coated magnetic beads) can be purchased as stand-alone products
  • riboPOOLs are shipped freeze-dried with a tube of nuclease-free water for safe resuspension
  • riboPOOLs come in 12, 24, and 96 reaction sizes.
  • Download our Protocol.

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Simple workflow with riboPOOLs


The riboPOOL workflow has four main steps:
1. Preparation of streptavidin-coated magnetic beads and riboPOOL
2. Hybridization of riboPOOL to target RNA
3. rRNA depletion
4. RNA Clean up.

All four steps can be completed within 70 minutes.

Achieve a fast and easy rRNA removal with riboPOOLs thanks to a hybridization-based workflow.

Our riboPOOL workflow allows a wide RNA-input range between 10 ng and 3 µg. When using >3 μg of total RNA for rRNA removal, please contact us for tips and tricks.

A huge benefit from our hybridization-based rRNA depletion approach is a higher correlation (R > 0.9) between non-depleted and depleted samples. Moreover, the riboPOOL workflow is completely automation-friendly.

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riboPOOLs Special Applications

riboPOOLs can be customized to fit your RNA samples. We create riboPOOLs for any mixture of RNA (e.g., Seawater samples), strongly degraded RNA (i.e., FFPE samples), or ribosome profiling (Ribo-Seq) samples

FFPE samples & degraded RNA samples


Total RNA extracted from FFPE tissue (Formalin-fixed, paraffin-embedded tissues) are heavily degraded, with RIN values below 2.
Due to their strong fragmentation, ribosomal RNAs are difficult to remove before RNA sequencing (RNA-Seq).
With a gapless and tiled probe coverage of the entire rRNA sequence, siTOOLs Biotech developed an efficient rRNA depletion tool for FFPE and other strongly degraded RNA samples.
We currently have human, mouse/rat, Caenorhabditis elegans, and Drosophila melanogaster riboPOOLs for degraded RNA samples.

Ribosome Profiling (Ribo-Seq)

Ribosome Profiling (Ribo-Seq) identifies actively translated RNAs by sequencing only those 30-base mRNA fragments protected by ribosomes.
The nuclease digest, degrading unprotected mRNA outside of ribosomes, also generates highly abundant ribosomal RNA contaminations, making up many sequencing reads.
siTOOLs Biotech has generated an efficient Ribo-Seq riboPOOL targeting primarily those extremely abundant rRNA contaminants commonly found in Ribo-Seq samples.
The entire rRNA sequence is covered with capture probes to deplete any less abundant rRNA fragment.
Our Ribo-Seq riboPOOL portfolio includes rRNA removal solutions for human, mouse/rat, Drosophila melanogaster, and Caenorhabditis elegans Ribo-Seq samples.

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What Customers Say:

Oxford Nanopore Sequencing

"We have tried Thermo RiboMinus Plant Kit and riboPOOL probe targeting Pan-plant to remove rRNA. It is necessary to perform two rounds of rRNA depletion with Thermo RiboMinusTM Plant Kit. Only one round is needed for riboPOOL probe." 
Y. Long (Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China)

Ribosome Profiling (Ribo-Seq)

"We are doing a lot of ribosome profiling experiments - mainly using mouse tissues and cell lines - and were in need of a ribosomal RNA depletion tool that was robust, economical, and adaptable.
Initially, we asked siTOOLs Biotech to design specific antisense probes against the most abundant rRNA contaminants that we tended to see in our ribosome profiling data, and that severely reduced the amount of usable reads.
The probes reduced the ribosomal RNAs they were designed for very well, however (and probably as to be expected) other rRNA contaminants subsequently became predominant and we needed a more uniform, rational tool that would cover all rRNA contaminants. 
Hence, siTOOLs Biotech designed and produced a ribosomal RNA depletion kit depleting both extremely abundant rRNA contaminants and less abundant ones.
We are very happy with the support, reactivity, and overall scientific expertise and knowledge of the siTOOLs team, which allowed us to have a great tool for a variety of experiments ongoing in the lab."
David GATFIELD (University of Lausanne, Center for Integrative Genomics (CIG)) Publication: Bhat et al. (Gatfield) (2021) Science


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