rRNA Depletion Kit
riboPOOLs
Our high-performance rRNA depletion kits remove unwanted ribosomal RNA (rRNA) from total RNA samples. As a result, they improve data quality and enable clearer insights for whole transcriptome sequencing (RNA-Seq). In addition, they support demanding applications such as ribosome profiling (Ribo-Seq).
Any species
Choose from over 70 species-specific riboPOOLs or request a custom design
Enzyme-free protocol
No RNase H, no 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
Ribosomal RNA Depletion for RNA-Seq, Ribo-Seq, and Transcriptome Analysis
The classic riboPOOL rRNA depletion kit (10 ng–3 µg input) efficiently removes ribosomal RNA (rRNA) from total RNA samples. As a result, it prevents rRNA from dominating sequencing reads and improves usable data for RNA-Seq, gene expression analysis, and whole transcriptome sequencing. In addition, rRNA depletion enriches both coding and non-coding transcripts. This leads to better read depth, higher transcript detection sensitivity, and improved sequencing efficiency.
Compared with poly(A) enrichment, rRNA depletion provides broader transcriptome coverage. It retains non-polyadenylated RNA, such as lncRNA, circRNA, precursor transcripts, and bacterial RNA. Therefore, it is ideal for degraded RNA samples, FFPE samples, and mixed-species samples like host–microbiome studies. Moreover, the rRNA-depleted RNA is compatible with Illumina short-read sequencing and Oxford Nanopore long-read sequencing. This enables flexible and reliable transcriptomics applications across many research areas.
Ribosomal RNA Depletion for Ribo-Seq and Ribosome Profiling Applications
Ribosome profiling (Ribo-Seq) is a powerful next-generation sequencing (NGS) method used to study protein synthesis and translation. It works by isolating and sequencing ribosome-protected fragments (RPFs), which are short RNA sequences (~30 nucleotides) bound by ribosomes. As a result, researchers can capture a real-time snapshot of active translation and measure how efficiently genes are translated into proteins.
With effective rRNA depletion, Ribo-Seq data quality improves significantly. This is because fewer sequencing reads are wasted on ribosomal RNA (rRNA), allowing better coverage of mRNA translation events. Therefore, rRNA depletion kits like riboPOOLs are essential for reliable Ribo-Seq workflows.
Key Ribo-Seq applications include:
- Quantifying protein synthesis and translation efficiency
- Identifying novel open reading frames (ORFs) and translation start sites
- Comparing transcription vs. translation rates to study gene regulation
To learn more about the Ribo-Seq riboPOOL workflow and available species, click here.
Data: How our riboPOOLs work
Decoreras leave (slug)
Eukaryote | RNA-Seq
Haloferax volcanii
Prokaryote | RNA-Seq
Pinus sylvestris
Eukaryote + Prokaryote | RNA-Seq
Staphylococcus aureus
Prokaryote | RNA-Seq
Toxoplasma gondii
Eukaryote | Ribo-Seq
Downloads
FAQ: Ribodepletion for RNA-seq and Ribo-seq
Can riboPOOLs be used with degraded RNA?
Standard RNA-Seq riboPOOLs perform best with DNA-free, high-quality RNA (RIN ≥ 7). However, as RNA degradation increases, pulldown efficiency may decrease. Nevertheless, the high complexity of riboPOOLs helps to compensate for this effect. In addition, a dedicated FFPE/degraded RNA riboPOOL may be available for your species.
My sample has < 100 ng of RNA, can I still use riboPOOLs?
RiboPOOLs perform well with input amounts down to 10 ng total RNA. For inputs below 10 ng, however, we recommend reducing the riboPOOL probe amount to ~30 pmol per reaction. To achieve this, resuspend the riboPOOL in 3× the recommended volume of nuclease-free water. Then, use 1 µl of the diluted solution per reaction.
Can riboPOOLs be used for ribosome profiling samples?
In Ribo-Seq experiments, a large fraction of reads typically consists of ribosomal RNA (rRNA). As a result, ribosome-protected fragments (RPFs) often account for less than 5% of total reads. To address this, our Ribo-Seq riboPOOLs are specifically designed to remove rRNA efficiently. Consequently, they significantly increase RPF mapping rates. You can explore our Ribo-Seq riboPOOLs portolio or request a custom design for your species.
Which RNA-Seq library preparation kits are compatible with riboPOOLs?
RiboPOOLs are compatible with most RNA-Seq library preparation kits. However, for optimal performance, we recommend using our ARGO Library Preparation Kit. This ensures seamless integration and consistent results across workflows.