riboPOOL



riboPOOLs

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
Cost-effective

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

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World Leading Scientist publish with riboPOOLs


 

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

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

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

 

Ribosome profiling


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

 


Specific, efficient rRNA depletion with riboPOOLs


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

riboPOOL

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

riboPOOL

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Reproducible results with riboPOOLs



High reproducibility between biological replicates with human riboPOOLs

riboPOOL

High reproducibility between biological replicates with mouse riboPOOLs

riboPOOL

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rRNA depletion for your species



Pan-riboPOOLs


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-riboPOOLs


Pan-Prokaryote riboPOOL (Bacteria and Archaea)
Bacteria
Pan-Bacteria riboPOOL
(Gram Positive and Gram negative Bacteria)
Archaea
Pan-Archaea riboPOOL
Plants
Pan-Plant riboPOOL »
Vertebrata
Pan-Bird riboPOOL
Pan-Mammal riboPOOL
Porifera
Pan-Sponge riboPOOL
Fungi
Pan-Fungi riboPOOL
Other
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


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

Archaea
Haloferax volcanii

Plants
Oryza sativa
Arabidopsis thaliana

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

Porifera
Amphimedon queenslandica

Fungi
Saccharomyces cerevisiae
Filamentous-Fungi
Pichia pastoris
Staphylococcus aureus
Ustilago maydis
Schizosaccharomyces pombe


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

Cephalochordata
Danio rerio

Platyhelminthes
Schmidtea mediterranea

Mollusca
Crassostrea gigas
Loripes orbiculatus and
Lucinoma aequizonata (Clamps)

Other:
Chlamydomonas reinhardtii
Emiliania huxleyi
human Globin mRNA
SARS-CoV-2 RNA


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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?



riboPool

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


riboPOOL

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



riboPOOL

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)



riboPOOL
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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