RNA depletion solutions for common NGS workflow challenges
NEXTFLEX RiboNaut rRNA Depletion Kit
For total RNA-seq workflows, the NEXTFLEX RiboNaut rRNA Depletion Kit removes cytoplasmic and mitochondrial rRNA from human, mouse, and rat total RNA. The kit uses subtractive hybridization with biotinylated probes and magnetic-bead capture to generate rRNA-depleted RNA that can proceed into downstream RNA-seq library preparation.
RiboNaut is well suited for broad transcriptome profiling when researchers need to retain mRNA and non-polyadenylated RNA species, including long non-coding RNAs and precursor transcripts. The workflow supports 5 ng to 1 µg total RNA input and can be used with low-input total RNA workflows.
NEXTFLEX Cas9-gRNA rRNA Depletion Enzyme
The NEXTFLEX Cas9-gRNA rRNA Depletion Enzyme provides a targeted approach for reducing rRNA-derived sequences from human, mouse, and rat RNA-seq libraries. The enzyme includes guide RNAs targeting nuclear rRNA loci, including 5S, 5.8S, 18S, 28S, and 45S, as well as mitochondrial 12S and 16S rRNA loci.
This option is useful when researchers want HMR rRNA depletion in a modular format that can be incorporated into an existing RNA-seq library workflow. It is designed to reduce rRNA-derived reads without requiring a specific library prep kit.
NEXTFLEX Cas9-gRNA Globin Depletion Enzyme
The NEXTFLEX Cas9-gRNA Globin Depletion Enzyme is designed for human blood and blood-derived RNA-seq libraries where globin transcripts consume a large fraction of sequencing reads. The guide RNA pool targets major human globin loci, including HBA1, HBA2, HBB, and HBD.
By reducing globin-derived reads, this enzyme helps increase the fraction of sequencing output available for non-globin transcripts. It is especially relevant for blood RNA-seq workflows where high hemoglobin transcript content can reduce sensitivity for gene expression analysis.
NEXTFLEX Cas9-gRNA Mito Depletion Enzyme
The NEXTFLEX Cas9-gRNA Mito Depletion Enzyme is designed to reduce human mitochondrial-derived sequences from NGS libraries. This includes mitochondrial-derived reads that can consume sequencing capacity in RNA-seq, ATAC-seq, DNA-seq, single-cell, or other human library workflows.
Use this option when high mitochondrial read content reduces the proportion of reads available for non-mitochondrial library content. By reducing mitochondrial-derived sequences, the enzyme can help improve usable sequencing output in workflows where mitochondrial background limits analysis.
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FAQs
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When should I use RNA depletion instead of poly(A) selection?
Use RNA depletion when you want broader transcriptome coverage beyond mature polyadenylated mRNA. rRNA depletion can support total RNA-seq workflows where non-polyadenylated transcripts, precursor RNAs, long non-coding RNAs, or fragmented RNA species may be relevant to the study. Poly(A) selection is a better fit when the goal is to enrich primarily for mature polyadenylated mRNA from high-quality eukaryotic RNA.
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How do I choose between NEXTFLEX RiboNaut and the NEXTFLEX Cas9-gRNA rRNA Depletion Enzyme?
Both are designed for human, mouse, and rat rRNA depletion. Choose NEXTFLEX RiboNaut when you want a probe-based approach that removes rRNA from total RNA before library preparation. Choose the NEXTFLEX Cas9-gRNA rRNA Depletion Enzyme when you want a targeted, modular depletion approach that can be incorporated into an existing RNA-seq library workflow.
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When is globin depletion useful for RNA-seq?
Globin depletion is useful for blood and blood-derived RNA-seq samples where hemoglobin transcripts can represent a large fraction of sequencing reads. Reducing globin-derived reads can help increase the fraction of sequencing output available for non-globin transcripts and improve the efficiency of gene expression analysis.
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When should I consider mitochondrial-derived sequence depletion?
Mitochondrial-derived sequence depletion may be useful when mitochondrial reads consume a large fraction of sequencing output and reduce the proportion of reads available for non-mitochondrial library content. This can be relevant for RNA-seq, single-cell workflows, ATAC-seq, DNA-seq, or other human NGS libraries with high mitochondrial background.
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Can RNA depletion improve detection of low-abundance transcripts?
RNA depletion can improve the proportion of sequencing reads available for lower-abundance RNA species by reducing highly abundant sequences such as rRNA or globin transcripts. The impact depends on the sample type, depletion target, library composition, and sequencing depth.
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Are these depletion solutions species-specific?
Yes, species compatibility matters. The rRNA depletion solutions on this page are designed for human, mouse, and rat samples. The globin and mitochondrial depletion enzymes are designed for human sequences. Customers working with other species or complex sample types should confirm fit before selecting a depletion product.
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Can targeted depletion be added to an existing RNA-seq workflow?
Yes, Cas9-gRNA depletion enzymes are designed as modular depletion tools that can be incorporated into existing NGS library workflows. This can be useful when a specific abundant sequence class, such as rRNA, globin, or mitochondrial-derived content, is reducing usable sequencing output.
