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NEXTFLEX Cas9-gRNA rRNA Depletion Enzyme (HMR)

The NEXTFLEX™ Cas9-gRNA Depletion Enzyme (HMR rRNA)powered by Jumpcode^® DepleteX™ technology, is a standalone, workflow-agnostic depletion enzyme that removes ribosomal RNA sequences from human, mouse, or rat libraries. You can drop it into any bulk or single cell RNA-seq workflow, increasing usable reads for informative transcripts and improving coverage across the transcriptome.

NEXTFLEX Cas9-gRNA Depletion Enzyme is provided at 5.6 μM and includes 435 unique guide RNAs targeting nuclear 5S, 5.8S, 18S, 28S, 45S and mitochondrial 12S and 16S rRNA loci. It requires a simple one-hour incubation making integration straightforward in pre- or post-PCR cleanup steps depending on your workflow. Designed to be highly cost-competitive and universally compatible, it delivers robust rRNA depletion without locking you into a specific library prep kit.

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Product variants

Unit Size: 50 μL

Part #:

NOVA-801100

Unit Size: 250 μL

Part #:

NOVA-801500

For research use only. Not for use in diagnostic procedures.

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Product information

Overview

Ribosomal RNA can account for more than 90% of reads in total RNA sequencing libraries, making depletion essential for detecting low-abundance, biologically relevant transcripts. The NEXTFLEX Cas9-gRNA Depletion Enzyme (HMR rRNA) is a cost-effective, workflow-independent, and highly specific enzyme that boosts usable reads without requiring you move to a new library prep kit. It implements a DASH (Depletion of Abundant Sequences by Hybridization) CRISPR depletion approach, using a precomplexed Cas9 and a pool of guides to cleave human, mouse, and rat rRNA sequences at the dsDNA stage. Whether you use your own prep method or a third-party kit, this module gives you clean, reproducible results backed by the performance of DepleteX™ technology.

Powered by Jumpcode™ technology for specific rRNA removal.
Ready-to-use: Provided as a Cas9-gRNA complex with integrated RNase inhibitor and Cas9 Buffer
Fast: Short one hour reaction time with only 5 minutes of hands-on time
Convenient: Easily fit into any library prep workflow
Flexible: Compatible with short and long-read sequencing
Automation-compatible – easily incorporated into manual or automated workflows

Additional product information

Cas9–gRNA-mediated targeted depletion

This kit applies Jumpcode® DepleteX™ technology to deplete rRNA sequences at the dsDNA stage, giving you flexibility in where the cut happens, either after second-strand synthesis or after library prep, depending on your workflow. The pre-complexed Cas9 and guide RNA pool targets conserved ribosomal RNA using 435 guides designed against GRCh38-annotated nuclear (5S, 5.8S, 18S, 28S, 45S) and mitochondrial (12S, 16S) rRNA. The pool has been functionally validated with good depletion performance in human, mouse, rat, dog and chicken libraries. Guides with predicted off-targets in protein-coding genes or other transcripts were remove to preserve informative content. This approach minimizes rRNA carryover and enhances the efficiency of total RNA sequencing without altering upstream chemistry.

A unit of NEXTFLEX Cas9-gRNA Depletion Enzyme is defined as the amount needed to deplete our recommended input of 1-10 ng of target dsDNA, assuming a library size of ≥400 bp (which typically corresponds to an insert of ~300 bp or greater).

Compatible with any RNA-seq strategy

Unlike depletion modules embedded in fixed library prep kits, this enzyme is completely workflow-agnostic. As long as you have double-stranded DNA, you can use it. By working at the dsDNA level, it sidesteps RNA input compatibility and integrates cleanly with existing RNA-seq workflows, no matter what reagents or sequencing downstream you're using.

Looking for a complete RNA-seq solution?

This depletion module is fully compatible with the NEXTFLEX Rapid Directional RNA-seq kits. Whether you’re working with intact samples or degraded RNA, Revvity offers RNA-seq workflows that deliver robust performance, high mapping rates, and flexible input requirements. Pair this module with a complete NEXTFLEX prep kit to streamline your workflow, improve data quality, and ensure end-to-end support from rRNA removal to sequencing-ready libraries.

Specifications

Other specifications

Shipping Conditions	Shipped in Dry Ice
Unit Size	250 μL

FAQs

What are the benefits of using CRISPR-based ribodepletion solutions?

CRISPR-based ribodepletion offers specific and efficient removal of rRNA sequences, improving transcriptome coverage and data quality. This approach helps preserve rare and fragmented transcripts, making it ideal for low-quality or low-input RNA samples. Additionally, it reduces off-target effects compared to traditional methods and streamlines workflows by integrating seamlessly into existing sequencing pipelines.
What is the benefit of depleting rRNA-derived fragments during library construction instead of before it?

Most commercially available rRNA depletion kits remove rRNA and mitochondrial rRNA at the RNA stage. However, this approach can be problematic when working with low-quality or low-input RNA, as it increases the risk of degrading rare or low-abundance transcripts due to RNA’s inherent instability.

The NEXTFLEX Cas9-gRNA Depletion Enzyme (HMR rRNA) addresses this challenge by removing rRNA-derived fragments after they are converted into dsDNA. This strategy minimizes degradation risks and preserves fragments from degraded samples, often lost with traditional pre-library depletion methods.
What species are compatible with the NEXTFLEX Cas9-gRNA Depletion Enzyme (HMR rRNA)?

The NEXTFLEX Cas9-gRNA Depletion Enzyme effectively depletes rRNA from human, mouse, and rat libraries. it has also shown good depletion performance with dog and chicken libraries.
What library prep kits are the NEXTFLEX Cas9-gRNA Depletion Enzyme (HMR rRNA) compatible with?

The NEXTFLEX Cas9-gRNA Depletion Enzyme (HMR rRNA) is compatible with libraries prepared using most widely used commercial library prep kits, including the NEXTFLEX Rapid Directional RNA-seq kit 2.0, and home-grown protocols..
Is the NEXTFLEX Cas9-gRNA Depletion Enzyme (HMR rRNA) compatible with degraded or fragmented RNA?

Yes, the NEXTFLEX Cas9-gRNA Depletion Enzyme (HMR rRNA) effectively depletes rRNA-derived fragments from libraries generated using degraded or fragmented RNA, making it suitable for challenging sample types.
Is this compatible with DASH workflows?

Yes. DASH refers to CRISPR-Cas9 depletion of abundant sequences in sequencing libraries. This product is a ready-to-use Cas9-gRNA complex for DASH-style rRNA removal from human, mouse, and rat libraries, with a simple one-hour incubation and drop-in placement before or after PCR. Because guides are included and pre-complexed, targeting is fixed to rRNA for these species.