riboPOOL rRNA Depletion Kit

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


riboPOOLs Benefit 1rRNA depletion for any species
riboPOOLs Benefit 2High complexity probes for efficient, reliable rRNA removal
riboPOOLs Benefit 3Cost-effective

riboPOOLs Benefit 4Wide RNA-input range (10 ng ‚Äď 3 ¬Ķg)
riboPOOLs Benefit 5riboPOOLs for highly degraded samples (FFPE)
riboPOOLs Benefit 6special solution for ribosome profiling

 


How do riboPOOLs work?



riboPOOL Pack Hunter Approach

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 3 key features:


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.


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


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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World Leading Scientists Publish with riboPOOLs


Biomolecules
Pastor et al. (2022) Comparative Analysis of rRNA Removal Methods for RNA-Seq Differential Expression in Halophilic Archaea
 
Scientific Reports
Wahl et al. (2022) Comparison of rRNA depletion methods for efficient bacterial mRNA sequencing

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

Ribosome Profiling

Science
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

Nature Protocols 
Galmozzi, C. V. et al. (2019) Selective ribosome profiling to study interactions of translating ribosomes in yeast 

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

Read more publications on riboPOOLs

 


Webinar: riboPOOLs - rRNA Depletion Kit for Any Species



 


Specific, efficient rRNA depletion with riboPOOLs

How riboPOOLs compare with Ribo-Zero

blue line

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

riboPOOL Human

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

riboPOOL Mouse

 


Reproducible results with riboPOOLs

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High reproducibility between biological replicates with human riboPOOLs

riboPOOL Human Results

High reproducibility between biological replicates with mouse riboPOOLs

riboPOOL Mouse Results

 


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)
Pan-Actinobacteria riboPOOL
Archaea
Pan-Archaea riboPOOL
Plants
Pan-Plant riboPOOL »
Vertebrata
Pan-Bird riboPOOL
Pan-Mammal riboPOOL

Porifera
Pan-Sponge riboPOOL
Fungi
Pan-Fungi riboPOOL
Filamentous-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.




Single Species riboPOOLs


Bacteria
Escherichia coli
Bacillus subtilis
Caulobacter crescentus
Clostridium perfringens
Stenotrophomonas sp.
Salmonella enterica
Pseudomonas aeruginosa


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
Apis mellifera
Argiope bruennichi


Cephalochordata
Danio rerio

Platyhelminthes
Schmidtea mediterranea

Mollusca
Crassostrea gigas
Loripes orbiculatus and
Lucinoma aequizonata (Clamps)


Algae:
Chlamydomonas reinhardtii
Cyanidioschyzon merolae
Emiliania huxleyi

Nematoda:
Caenorhabditis elegans NEW

Other:
human Globin mRNA
SARS-CoV-2 RNA



Special Applications riboPOOLs


FFPE samples & degraded RNA samples

FFPE riboPOOLs cover the entire rRNA sequence with tiled oligos

Ribosome Profiling (Ribo-Seq)

Ribo-Seq riboPOOLs cover the entire rRNA sequence with tiled oligos plus the overrepresented rRNA contaminants that are unique to ribosome profiling

Degraded RNA (FFPE samples) or ribosome profiling RNA can be processed with our special applications riboPOOLs.




Special Applications riboPOOLs



FFPE /degraded
riboPOOLs



Vertebrata
human
human-mouse-rat
mouse-rat


Nematoda
Caenorhabditis elegans

Arthropoda
Drosophila melanogaster


 

Ribo-Seq
riboPOOLs



Vertebrata
human
human-mouse-rat
mouse-rat


Nematoda
Caenorhabditis elegans

Arthropoda
Drosophila melanogaster


 

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.

 


Find the right riboPOOLs Kit & Probes



riboPOOL kits


riboPOOL probes

  • riboPOOLs can be purchased as stand-alone products
  • riboPOOLs are shipped shipped as liquid 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 Workflow

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 ¬Ķg. When using >3 őľg 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



Representative Bioanalyzer Analysis of RNA with varying RNA Quality

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)



rRNA DEpletion with riboPOOLs
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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News



             
 

What Customers Say:

 

RNA Sequencing

“Our group works with halophilic archaea and the main challenge for prokaryotic transcriptomics is the low rRNA:mRNA ratio. siTOOLs Biotech has custom-design probes that target Haloferax volcanii (HVO) and the Pan-Archaea riboPOOL for ribodepletion in a broad spectrum of archaea. Both riboPOOLs efficiently depleted > 90% of rRNA across the different species of halophilic Archaea (Halobacterium salinarum, Haloferax mediterranei and Haloarcula hispanica). The use of rRNA removal kits, like riboPOOLS can greatly help facilitate rapid progress in understanding the transcriptional response of a wide diversity of archaea to their environment”.
Dr. Mar Martinez-Pastor (Senior Scientist, Schmid Lab, Duke University)
Publication: Pastor et al. (2022) Biomolecules


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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