riboPOOLs rRNA depletion for any species

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)

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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

  • Wide RNA-input range (10 ng – 3 µg)

  • High complexity probes for efficient, reliable rRNA removal

  • riboPOOLs for highly degraded samples (FFPE)

  • Cost-effective

  • special solution for ribosome profiling

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.

Single Species riboPOOLs


Escherichia coli

Bacillus subtilis

Caulobacter crescentus

Clostridium perfringens

Stenotrophomonas sp.

Salmonella enterica

Pseudomonas aeruginosa


Drosophila melanogaster

Plautia stali

Leptinotarsa decemlineata

Ixodes scapular

Aedes albopictus

Apis mellifera

Argiope bruennichi


Haloferax volcanii


Danio rerio


Oryza sativa

Arabidopsis thaliana


Schmidtea mediterranea


Mus musculus / R. norvegicus

Homo sapiens sapiens

Chinchilla lanigera

Gallus gallus domesticus


Crassostrea gigas

Loripes orbiculatus and

Lucinoma aequizonata (Clamps)


Amphimedon queenslandica


Chlamydomonas reinhardtii

Cyanidioschyzon merolae

Emiliania huxleyi


Saccharomyces cerevisiae


Pichia pastoris

Staphylococcus aureus

Ustilago maydis

Schizosaccharomyces pombe


human Globin mRNA


Specific, efficient rRNA depletion with riboPOOLs


Reproducible results with riboPOOLs


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


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) 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.


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.

World Leading Scientist publish with riboPOOLs

scientific reports

Puiggené, Ò. et al. (2022) Extracellular degradation of a polyurethane oligomer involving outer membrane vesicles and further insights on the degradation of 2,4-diaminotoluene in Pseudomonas capeferrum TDA1 

nature communications

M. A. Lawlo et al (2021) A transposon expression burst accompanies the activation of Y-chromosome fertility genes during Drosophila spermatogenesis

Genome Biology

Weipeng Mo et al. (2021) Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing

Dimitar Plamenov Petrov et al. (2021) Quantitative  profiling  and  dynamics  of  mRNA  modifications  in  Escherichia coli

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


Felix Grünberger et al. (2021) Nanopore sequencing of RNA and cDNA molecules in Escherichia coli 

Microbiology Spectrum

Martin Gélinas et al. (2021) The de novo Purine Biosynthesis Pathway Is the Only Commonly Regulated Cellular Pathway during Biofilm Formation in TSBBased Medium in Staphylococcus aureus and Enterococcus faecalis 

bioRxiv - preprint

Weihua Qin et. Al (2022) Probing protein ubiquitination in live cells 

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