rRNA accounts for a high proportion of Total RNA in organisms, but it can provide little effective information. These Rnas will produce a large number of invalid data, which is of little significance for the study of obtaining biological information. Meanwhile, rRNA with a high proportion makes mRNA relatively abundant in transcripts low, thus affecting the detection of transcripts with low abundance. Therefore, in conventional RNA sequencing (RNA-SEQ), the effective removal of rRNA is essential to achieve cost-effective sequencing of RNA.
Figure 1. Pie chart showing the distribution of different RNA types in total RNA extracted from human tissues or cells.
rRNA Removal Methods
For samples that lack a poly(A) tail—such as prokaryotic RNA or degraded total RNA (e.g., FFPE samples)—poly(A)-based enrichment is not possible. In these cases, rRNA removal is used to enrich for mRNA.
|
Category |
Probe Hybridization (Ribo-Zero) |
RNase H Digestion(Most commonly used) |
One-Step rRNA Block (RT Blockers) |
Magnetic Bead-based rRNA Removal |
|
Principle |
Species-specific probes hybridize with rRNA, removed via streptavidin beads. |
DNA probes + RNase H digest rRNA in DNA-RNA hybrids. |
Blocker probes prevent reverse transcription of rRNA. |
Biotin probes hybridize to rRNA, removed via magnetic beads. |
|
Advantages |
High efficiency, good specificity, works across species. |
High specificity, efficient, works across species. |
Fast (3 min), simple one-step, no purification, high detection. |
Highly efficient, broad species compatibility, high specificity. |
|
Limitations |
Requires species-specific probes. |
Requires species-specific DNA probes. |
Needs specialized kits. |
Higher cost. |
Figure 2. Schematic illustration of rRNA removing
MaxUp Series rRNA Depletion Kit
The MaxUp series rRNA depletion reagents utilize RNase H–based digestion to selectively remove ribosomal RNA (rRNA) from total RNA, preserving messenger RNA (mRNA) and other non-coding RNAs. This system supports a wide range of sample types and input amounts, completing the entire workflow in under 2 hours with less than 10 minutes of hands-on time.
MaxUp is highly effective for both standard and challenging samples, including degraded RNA such as FFPE specimens, ensuring efficient rRNA removal. By increasing the proportion of informative reads in sequencing data, it enables cost-effective, high-quality RNA sequencing across diverse sample types.
Why MaxUp Works
RNase H–based rRNA depletion is the preferred approach for RNA-seq, especially for partially degraded samples. Unlike other methods, RNase H digestion maintains RNA integrity while selectively removing rRNA, maximizing usable sequencing data and improving downstream analysis. The MaxUp workflow leverages this principle to deliver reliable and reproducible rRNA removal for a wide variety of research and clinical applications.
Performance Highlights
The MaxUp series not only simplifies the workflow but also delivers consistent, high-quality results. Extensive validation across different sample types demonstrates:
- High rRNA Removal Efficiency: Efficiently depletes rRNA from total RNA, even in degraded or low-input samples such as FFPE.
- Broad Sample Compatibility: Works with a wide range of species and RNA qualities.
- Rapid and User-Friendly: Complete workflow under 2 hours, with less than 10 minutes of hands-on time.
- Enhanced Sequencing Data: Significantly increases the proportion of informative reads, improving library complexity and reducing sequencing costs.
Product Performance
(1) Plant Samples
Total RNA from plant samples was treated with RNase H to selectively remove ribosomal RNA (rRNA). qPCR analysis was then used to compare rRNA and mRNA levels before and after depletion. The results demonstrate that the MaxUp rRNA Depletion Kit effectively removes rRNA from plant RNA while preserving mRNA.
Figure 3. Efficient rRNA Removal using MaxUp rRNA Depletion Kit (Plant)
This product has been verified for species including Arabidopsis, rice, wheat, cotton, corn, rapeseed, sunflower, tomato, walnut, strawberry, watermelon, barley, sweet potato, potato, mulberry, etc.
(2) Human, Rat, and Mouse Samples
Total RNA from human, rat, and mouse samples was subjected to RNase H–based rRNA removal, followed by library construction and sequencing. Data analysis confirmed that the kit efficiently depletes rRNA, resulting in higher-quality sequencing libraries with increased informative read content.
1.Broad Compatibility Across Input Amounts and Sample Types
Figure 4. Efficient rRNA Removal Across Multiple Sample Types and Input Amounts
Library preparation was performed using 12726 and RNA Library Preparation Kit (Cat#12308, with strand-specific protocols) on various RNA sample types—including human, mouse, and rat total RNA—across different input amounts (100 ng to 1 μg). The rRNA residual rate remained consistently low and was significantly reduced compared to Supplier V* across all sample types and input levels.
Figure 5. Comparison of rRNA Removal Efficiency by Sequencing and qPCR
Using 1 μg of 293T total RNA, samples were processed by oligo-dT enrichment or rRNA depletion. Sequencing measured residual rRNA%(A). qPCR targeting cytoplasmic (18S, 28S, 5.8S) and mitochondrial (12S, 16S) rRNAs showed significant Ct value increases after depletion(B), demonstrating effective rRNA removal.
Product list
|
Category |
Name |
Cat. No. |
Size |
|
|
RNA Lib Prep |
Dual-mode(Strand specific & Non Strand specific) |
12308ES24/96 |
24 T/96 T |
|
|
Premix version |
12340ES24/96 |
|||
|
12341ES24/96 |
||||
|
mRNA isolation |
Eukaryotic mRNA |
12629ES |
24 T/96 T |
|
|
rRNA depletion |
Human/Mouse/Rat |
Hieff NGS™ MaxUp Human/Mouse/Rat rRNA Depletion Kit(rRNA ITS/ETS) 2.0 |
12726ES |
|
|
Plant |
12254ES |
|||
|
Beads |
- |
12602ES |
1/5/60 mL |
|