NEBNext rRNA Depletion Kit
The NEBNext rRNA Depletion Kit (Human/Mouse/Rat) enables efficient removal of ribosomal RNA (rRNA) from total RNA for human, mouse and rat RNA samples.
This kit works well for both low-quality, degraded RNA (including FFPE RNA) and high-quality, intact RNA. rRNA depletion with a broad range of input amounts (10 ng to 1 μg) is completed in approximately 2 hours, with less than 10 minutes of hands-on time.
- Suitable for FFPE (degraded) or high-quality (intact) RNA
- 10 ng to 1 μg input
- Remove > 95% of rRNA, and obtain more relevant sequence reads from your sample
- Obtain a more complete transcriptome picture through retention of noncoding & incomplete RNAs that are lost with oligo d(T) poly(A) mRNA enrichment methods
- Suitable for use with human, mouse or rat samples
- Easily integrated upstream of any downstream random-primed cDNA synthesis protocol
- Also available with RNA Sample Purification Beads
Application Note:
Selective depletion of abundant RNAs to enable transcriptome analysis of low-input and highly-degraded RNA from FFPE breast cancer samples
NEBNext rRNA Depletion Kit Workflow
Click to enlarge
New: NEBNext RNA Depletion Core Reagent Set
In RNA-seq, highly expressed transcripts with minimal biological interest, such as ribosomal RNA (rRNA) can dominate readouts and mask detection of more informative low-abundance transcripts. This challenge is amplified when working with sample types for which pre-designed RNA depletion kits are not available. The NEBNext RNA Depletion Core Reagent set provides a customized approach to deplete unwanted RNA from any organism, using probe sequences designed with the user-friendly NEBNext Custom RNA Depletion Design Tool.
The efficient RNase-H-based workflow, and close tiling of probes designed using the online tool, enables effective depletion from both low- and high-quality RNA, with a broad range of input amounts.
The kit is also available with RNAClean® beads.
- Compatible with a broad range of input amounts: 10 ng - 1µg
- Suitable for low-quality or high-quality RNA
- Fast workflow: 2 hours, with less than 10 minutes hands-on time
New: NEBNext Globin & rRNA Depletion Kit
Globin mRNA and rRNA are highly abundant in blood samples, and their efficient and specific removal is desirable in order to reveal the biological significance of less abundant transcripts.
The NEBNext Globin & rRNA Depletion Kit (Human/Mouse/Rat) employs the NEBNext RNase H-based RNA depletion workflow to deplete globin mRNA, cytoplasmic rRNA and mitochondrial rRNA with human, mouse and rat samples, and is effective with intact and degraded RNA.
- Efficient, specific depletion of globin mRNA and rRNA
- Suitable for low-quality or high-quality RNA
- Compatible with a broad range of input amounts: 10 ng - 1 μg
- Optional integration with poly(A) mRNA isolation workflows for removal of globin RNAs, rRNAs, and noncoding RNAs
- Fast workflow: 2 hours, with less than 10 minutes hands-on time
- Also available with RNA Sample Purification Beads
New: NEBNext rRNA Depletion Kit (Bacteria)
Ribosomal RNA (rRNA) is highly abundant in bacterial samples, and its removal is desirable in order to reveal the biological significance of less abundant transcripts. Specific enrichment of bacterial mRNAs is challenging due to their lack of poly(A) tails, and so the converse – efficient and specific removal of bacterial rRNA – is necessary.
The NEBNext rRNA Depletion Kit (Bacteria) employs the NEBNext RNase H-based RNA depletion workflow to target removal of rRNA from gram-positive and gram-negative organisms. The method is effective with intact and degraded RNA, from monocultures or samples with mixed bacterial species (e.g., metatranscriptomic).
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„The NEB Bacterial Depletion has depleted rRNA equally or better than our previous ribodepletion gold standard across a wide RIN quality range. We have been pleased with the flexibility of Total RNA input ranges and have routinely gotten effective ribodepletion at 100 ng Total RNA Input in both single isolates and metagenomic samples. The protocol is also more ergonomically friendly than bead based ribodepletion protocols. Of all the new bacterial ribodepletion methods we have tested, NEB was by far the best.“ Research Assistant, Biomedical research institution |
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- Efficient, specific depletion of bacterial rRNA (5S, 16S, 23S)
- Compatible with both gram-positive and gram-negative organisms
- Effective with monocultures and mix of bacterial species (e.g., metatranscriptome)
- Compatible with a broad range of input amounts: 10 ng - 1 µg
- Suitable for low-quality or high-quality RNA
- Fast workflow: 2 hours, with less than 10 minutes hands-on time
New: NEBNext RNA Depletion Core Reagent Set
Introducing a new solution for customized depletion of abundant RNAs.
In RNA-seq, highly expressed transcripts with minimal biological interest, such as ribosomal RNA (rRNA) can dominate readouts and mask detection of more informative low-abundance transcripts. This challenge is amplified when working with sample types for which pre-designed RNA depletion kits are not available. The NEBNext RNA Depletion Core Reagent set provides a customized approach to deplete unwanted RNA from any organism, using probe sequences designed with the user-friendly NEBNext Custom RNA Depletion Design Tool.
The efficient RNase-H-based workflow, and close tiling of probes designed using the online tool, enables effective depletion from both low- and high-quality RNA, with a broad range of input amounts.
The kit is also available with RNAClean® beads.
RNA-seq samples can include a large dynamic range of transcript expression, and unwanted, abundant RNAs must be removed in order to achieve efficient sequencing of the RNAs of interest. While pre-designed kits are available for some sample types (e.g. human, mouse, rat, some bacteria) and abundant RNAs (e.g. rRNA, globin mRNA), a customized approach is required for rRNA removal from other sample types as well as for removal of specific non-rRNA RNAs.
- Customizable option to deplete unwanted RNA from any organism, using probe sequences designed with the NEBNext Custom RNA Depletion Design Tool.
- Compatible with a broad range of input amounts: 10 ng - 1 μg
- Suitable for low-quality or high-quality RNA
- Fast workflow: 2 hours, with less than 10 minutes hands-on time
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„The open-access tool to design sequences for rRNA removal that NEB is providing to the research community has been very useful for us. This method for customization of RNA depletion has proven valuable for a range of organisms. Use of custom probes for Xenopus laevis ribosomal RNA worked very well, resulting in complete depletion. And supplementing the probes in the NEBNext rRNA Depletion Kit (Bacteria) with custom probes for the bacillus Eggerthella lenta led to 90% depletion of the ribosomal RNA.“ Dr. Vladimir Benes, Head of Genomics Core Facility, EMBL, Heidelberg |
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„This technology has been superb for eliminating the ribosomal RNA for a range of custom projects, including tracking novel viruses in mosquitoes, longitudinal profiling for astronauts, and host-pathogen interactions in COVID samples. Any species can now have a rich, in-depth profile created of its complex transcriptome, from non-coding RNAs to RNA modifications“ Dr. Christopher Mason, Weill Cornell Medicine, New York (USA) |
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The NEBNext Custom RNA Depletion Design Tool was used to design probes against rRNA of the mosquito Aedes aegypti (28S, 18S, 5.8S, 5S, mt16S and mt12S), and the archaeal species Thermococcus kodakarensis and Pyrococcus furiosus (23S, 16S, 5SrRNA1, 5SrRNA2). Total RNA (1 µg, 100 ng or 10 ng) was used as input for rRNA depletion using the RNA Depletion Core Reagent Set with the designed probes. RNA-seq libraries were prepared using the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina® followed by paired-end sequencing (2 x 75 bp). 20 million reads were sampled (seqtk) from each library. Read pairs were identified as ribosomal using mirabait (6 or more shared 25-mers), and levels of rRNA remaining were calculated by dividing matched reads by the total number of reads passing instrument quality filtering. The data represents an average of 3 replicates. The method efficiently depletes targeted rRNA across species and a wide range of total RNA input amount (1 µg–10 ng).
Available products:
| PRODUCT | Prod. # | SIZE | PRICE | ||
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| NEBNext® RNA Depletion Core Reagent Set | E7865S | 6 rxns | 254 € |  |
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| E7865L | 24 rxns | 924 € | |
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| E7865X | 96 rxns | 3.326 € | |
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| NEBNext® RNA Depletion Core Reagent Set with Beads | E7870S | 6 rxns | 262 € | |
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| E7870L | 24 rxns | 963 € | |
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| E7870X | 96 rxns | 3.465 € | |
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| NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) | E7400S | 6 rxns | 297 € | |
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| E7400L | 24 rxns | 1.080 € | |
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| E7400X | 96 rxns | 3.885 € | |
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| NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) with Beads | E7405S | 6 rxns | 305 € | |
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| E7405L | 24 rxns | 1.125 € | |
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| E7405X | 96 rxns | 4.050 € | |
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| NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) | E6310S | 6 rxns | 330 € | |
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| E6310L | 24 rxns | 1.200 € | |
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| E6310X | 96 rxns | 4.320 € | |
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| NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) with Beads | E6350S | 6 rxns | 360 € | |
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| E6350L | 24 rxns | 1.324 € | |
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| E6350X | 96 rxns | 4.766 € | |
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| NEBNext® Globin & rRNA Depletion Kit (Human/Mouse/Rat) | E7750S | 6 rxns | 340 € | |
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| E7750L | 24 rxns | 1.235 € | |
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| E7750X | 96 rxns | 4.450 € | |
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| NEBNext® Globin & rRNA Depletion Kit (Human/Mouse/Rat) with RNA Sample Purification Beads | E7755S | 6 rxns | 350 € | |
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| E7755L | 24 rxns | 1.290 € | |
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| E7755X | 96 rxns | 4.635 € | |
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| NEBNext® rRNA Depletion Kit (Bacteria) | E7850S | 6 rxns | 297 € | |
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| E7850L | 24 rxns | 1.080 € | |
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| E7850X | 96 rxns | 3.885 € | |
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| NEBNext® rRNA Depletion Kit (Bacteria) with RNA Sample Beads | E7860S | 6 rxns | 305 € | |
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| E7860L | 24 rxns | 1.125 € | |
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| E7860X | 96 rxns | 4.050 € | |
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| Passend dazu: | |||||
| NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina | E7760S | 24 rxns | 1.028 € | |
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| E7760L | 96 rxns | 3.495 € | |
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| NEBNext® Ultra II RNA Library Prep Kit for Illumina® | E7770S | 24 rxns | 980 | |
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| E7770L | 96 rxns | 3.325 € | |
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| NEBNext® Poly(A) mRNA Magnetic Isolation Module | E7490S | 24 rxns | 69 € | |
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| E7490L | 96 rxns | 247 € | |
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As of: 01.01.2021
NEBNext products are available at a permanent low price that can not be further discounted.
Further information can be found in our Technical Resources section or at neb.com. Information on trademarks can be found here.
