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NEXTFLEX Cas9-gRNA Mito Depletion Enzyme (Human)

Name: NEXTFLEX Cas9-gRNA Mito Depletion Enzyme (Human)
Price: 500 USD
Availability: InStock

The NEXTFLEX™ Cas9-gRNA Mito Depletion Enzyme (Human) is a standalone, flexible CRISPR-Cas9 module that removes mitochondrial derived sequences from human NGS libraries. It can be added at the double-stranded DNA stage of existing ATAC-seq, DNA-seq, bulk RNA-seq, or single-cell workflows, reducing mitochondrial background so more reads are directed on nuclear genes, regulatory elements, and other loci of interest.

Supplied as a pre-complexed Cas9–guide RNA mixture, the NEXTFLEX Cas9-gRNA Mito Depletion Enzyme (Human) contains 657 guide RNAs targeting 17 mtDNA-encoded genes and selected nuclear mitochondrial pseudogenes. One unit is defined as the amount required to deplete 1–10 ng of target double-stranded DNA library of at least 400 bp. Designed for broad compatibility, it delivers efficient mitochondrial depletion across diverse human library types without locking you into a particular library preparation kit or sequencing platform.

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Feature	Specification
Automation Compatible	Yes
Product Group	RNA Depletion

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Product variants

Unit Size: 50 μL

Part #:

NOVA-803100

List price

USD 500.00

Your online price:

Unit Size: 250 μL

Part #:

NOVA-803500

List price

USD 2,500.00

Your online price:

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

Product information

Overview

Mitochondrial-derived fragments can account for a large share of reads in human ATAC-seq, DNA-seq, and bulk or single cell RNA-seq libraries, especially from mitochondria-rich tissues, reducing effective coverage of nuclear loci and low-abundance features. The NEXTFLEX Cas9-gRNA Mito Depletion Enzyme (Human) is a cost-effective, workflow-independent, and highly specific enzyme that reduces mitochondrial background, directing more sequencing capacity toward nuclear genes, regulatory elements, and other regions of interest, without requiring you to move to a new library prep kit.

It uses a DASH-style (Depletion of Abundant Sequences by Hybridization) CRISPR-Cas9 depletion approach, with a precomplexed Cas9 and pool of guides designed to cleave human mitochondrial DNA and selected nuclear mitochondrial pseudogenes at the double-stranded DNA stage. Whether you use your own prep method or a commercial kit, this module delivers clean, reproducible depletion of mitochondrial genome–derived sequences and improved coverage of nuclear content across diverse human NGS workflows.

Powered by Jumpcode™ DepleteX™ technology for specific mitochondrial sequence removal
Ready to use: provided as a Cas9-gRNA complex with integrated RNase inhibitor and 10X Cas9 Buffer
Fast: one-hour reaction time with only about 5 minutes of hands-on work
Convenient: easily fits into ATAC-seq, DNA-seq, RNA-seq, and single-cell workflows at the dsDNA stage
Flexible: compatible with short- and long-read sequencing
Automation-compatible: readily incorporated into manual or automated workflows

Additional product information

Cas9-gRNA-driven targeted mitochondrial depletion kit

The NEXTFLEX Cas9-gRNA Mito Depletion Enzyme (Human) is designed for datasets where mitochondrial reads stop being a minor annoyance and start consuming your experiment. In ATAC-seq, it removes the dominant mitochondrial peak that can soak up a large fraction of usable reads, sharpening nuclear open-chromatin profiles in mitochondria-rich tissues such as heart, muscle, or brain. In low-pass and whole-genome sequencing, it clears out the excess mitochondrial reads so more of your fixed sequencing budget is spent on nuclear chromosomes instead of mtDNA. For bulk and single-cell RNA-seq workflows, it cuts fragments derived from mitochondrial transcripts and mtDNA, reclaiming reads and redirecting them to nuclear genes that drive clustering, differential expression, and downstream biology. Because depletion occurs on double-stranded DNA, you can apply the enzyme either to amplified cDNA as part of a planned workflow or to completed libraries that turned out to be heavily mitochondrial, turning "high-mito" samples into usable data.

Bar chart showing percent mitochondrial reads in a human NGS library before and after treatment with the NEXTFLEX Cas9-gRNA Mito Depletion Enzyme (Human), dropping from 9.31% to 0.13%.

Figure 1. NEXTFLEX Cas9-gRNA Mito Depletion Enzyme (Human) dramatically reduces mitochondrial reads in NGS libraries obtained from a human tissue sample. Percent of reads mapped to the mitochondrial genome in an untreated library compared with the same library after depletion, showing a drop from 9.31% to 0.13% and freeing sequencing capacity for nuclear targets.

Mitochondrial depletion kit compatible with diverse human NGS workflows

Supplied as a standalone Cas9-gRNA complex rather than embedded in a specific library prep kit, the NEXTFLEX Cas9-gRNA Mito Depletion Enzyme (Human) can be added wherever your human samples have been converted to double-stranded DNA. You can introduce mitochondrial depletion into ATAC-seq, low-pass and whole-genome sequencing, targeted DNA panels, bulk, or single-cell RNA libraries without changing your upstream chemistry. Operating at the dsDNA stage avoids constraints around nucleic acid integrity or input type and keeps the module compatible with existing manual or automated workflows on both short- and long-read sequencing platforms.

Looking for an end-to-end NGS solution for mito depletion?

This mitochondrial depletion module works seamlessly with NEXTFLEX library prep solutions. Use NEXTFLEX kits to generate high quality DNA or RNA libraries from a broad range of inputs and sample qualities, then add the NEXTFLEX Cas9-gRNA Mito Depletion Enzyme (Human) to strip out mitochondrial background before sequencing. The result is a single, integrated workflow from sample to sequencing-ready library that increases the proportion of reads on nuclear targets and gives you one partner for chemistry, optimization, and technical support.

Specifications

Other specifications

Automation Compatible	Yes
Product Group	RNA Depletion
Shipping Conditions	Shipped in Dry Ice
Unit Size	50 μL

FAQs

What are the benefits of using CRISPR-based mitochondrial depletion in DNA and RNA NGS libraries?

CRISPR-based depletion uses a Cas9–guide RNA complex to recognize and cut molecules derived from the mitochondrial genome in already-prepared DNA- and RNA-derived dsDNA libraries. Removing these highly abundant fragments reduces the fraction of reads that land on mtDNA and mitochondrial transcripts, so more of your fixed sequencing budget is spent on nuclear genes, regulatory elements, and other loci of interest. Because depletion happens after conversion to double-stranded DNA, it also helps preserve material from low-input or partially degraded samples that might be lost with earlier, RNA-level depletion steps.
Why deplete mitochondrial genome–derived fragments at the dsDNA stage instead of at the RNA or genomic DNA stage?

Working at the dsDNA stage avoids repeated handling of fragile RNA and lets you treat the library only after you know it has high mitochondrial content. Traditional strategies that target RNA or genomic DNA can be sensitive to RNA integrity, extraction method, or cell type, and they can risk losing rare transcripts or introducing unwanted bias. Applying depletion to dsDNA libraries instead allows you to use your preferred extraction and library prep protocol, then remove mitochondrial fragments with a single incubate-and-clean-up step that slots into existing workflows.
Which species and sample types are supported for mitochondrial depletion?

The NEXTFLEX Cas9-gRNA Mito Depletion Enzyme (Human) is programmed specifically against human mitochondrial DNA and selected human nuclear mitochondrial pseudogenes. It is intended for human samples only and has been designed for use with a wide range of human library types, including ATAC-seq, low-pass or whole-genome DNA-seq, targeted panels, bulk RNA-seq, and single-cell or single-nucleus workflows once material has been converted to double-stranded DNA.
What library prep kits and sequencing platforms are compatible with the NEXTFLEX Cas9-gRNA Mito Depletion Enzyme (Human)?

Because depletion occurs on double-stranded DNA, this module is broadly compatible with most human DNA-seq and RNA-seq library prep kits, including NEXTFLEX Rapid XP v2 DNA-seq kits, NEXTFLEX Rapid Directional RNA-seq kits, and other commercial or in-house workflows that produce dsDNA libraries. It can be used ahead of short-read or long-read sequencing, and it is suitable for both manual and automated workflows, as long as you can introduce a one-hour incubation and a subsequent cleanup step.
Is the NEXTFLEX Cas9-gRNA Mito Depletion Enzyme (Human) suitable for degraded or low-input samples?

Yes. Because the depletion step is performed on dsDNA rather than on RNA, the module is well suited to low-input or partially degraded RNA or DNA samples that can still be converted into sequenceable libraries. The Cas9–gRNA complex acts on library fragments regardless of the original RNA integrity, so you can combine challenging samples with standard RNA-seq or DNA-seq workflows and then remove mitochondrial background at the library stage. As with any low-input application, we recommend monitoring library complexity and standard QC metrics.
How much mitochondrial reduction can I expect?

In internal testing on human libraries, treatment with the NEXTFLEX Cas9-gRNA Mito Depletion Enzyme (Human) has reduced mitochondrial reads from roughly 9% of total reads to well under 1%, corresponding to more than a 98% drop in mitochondrial fraction under recommended conditions. Actual depletion will depend on input amount, library design, tissue type, and the initial mitochondrial burden, so users may need to optimize enzyme-to-DNA ratios for their specific samples, especially when working at higher inputs.
Does mitochondrial depletion affect nuclear reads or introduce bias?

The guide RNA pool contains 657 unique guides targeting 17 mtDNA-encoded genes together with selected nuclear mitochondrial pseudogenes. This guide RNA pool was designed to avoid protein-coding nuclear genes outside of those pseudogene loci. As a result, the primary effect of the enzyme is to remove molecules derived from the mitochondrial genome while preserving nuclear content. As with any targeted depletion method, we recommend validating performance and checking for unexpected effects when working with unusual library designs, extreme GC content, or highly customized workflows.
Can this module be used in DASH-style workflows or alongside other Cas9-based depletion modules?

Yes. This product is a ready-to-use Cas9–guide RNA complex for DASH-style (Depletion of Abundant Sequences by Hybridization) removal of mitochondrial genome–derived fragments from human dsDNA libraries. It can be positioned before or after PCR, depending on your workflow, and can in principle be combined with other Cas9-based depletion modules that target different sequences, provided that reaction conditions and cleanup steps are carefully optimized so that each module performs as expected.
Can I use the NEXTFLEX Cas9-gRNA Mito Depletion Enzyme (Human) in single-cell or single-nucleus workflows?

Yes, as long as the material has been converted into a dsDNA library or amplified cDNA pool. The enzyme can be applied to human single-cell or single-nucleus ATAC-seq, RNA-seq, or multiome libraries to reduce mitochondrial reads that inflate mitochondrial QC metrics and consume sequencing depth. When using the module in single-cell workflows, it is important to interpret mitochondrial read percentages considering the depletion step and to confirm that cell calling and clustering behavior remain consistent with expectations.
Should I use this product if I want to study mitochondrial DNA variants, copy number, or heteroplasmy?

No. The NEXTFLEX Cas9-gRNA Mito Depletion Enzyme (Human) is designed to remove sequences derived from the mitochondrial genome. It is ideal for experiments where mitochondrial signal is a source of background noise, and the focus is on nuclear features. If your primary goal is to profile mtDNA variants, copy number, or heteroplasmy, you should not use this depletion module, or you should test substantially reduced enzyme levels to ensure that the mitochondrial reads you need are preserved.