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RiboCop rRNA Depletion Kit HMR V2

  • Depletion of all cytoplasmic and mitochondrial rRNA from human,
    mouse, or rat samples
  • NEW! Innovative probe design minimizing off-target effects
  • 1 ng to 1 µg total RNA input (FFPE compatible)

RiboCop for Human/Mouse/Rat V2

Total RNA from mammalian species is comprised of large amounts of undesired ribosomal RNA (rRNA) which accounts for ~80 – 90 % of all RNA. Lexogen’s RiboCop rRNA Depletion Kits for Human/Mouse/Rat remove undesired cytoplasmic (28S, 18S, 5.8S, and 45S rRNA) and mitochondrial rRNA (mt16S, mt12S, and 5S) from intact as well as degraded material, including formalin-fixed, paraffin-embedded (FFPE) samples.

RiboCop for Human/Mouse/Rat (HMR) V2 is offered as a stand-alone (Cat. No. 144) or as bundled version with CORALL RNA-Seq V2 (Cat. No. 183 – 184). RiboCop Kits are compatible with all random primed total RNA library prep kits.

Performance

Sequence what matters most! RiboCop enables specific, highly effective, non-enzymatic depletion of ribosomal RNA from a broad range of sample types, including low input, degraded, and FFPE samples.

Ribosomal RNA was depleted from Universal Human Reference RNA (UHRR) using RiboCop for Human/Mouse/Rat (HMR) V2 over a wide range of input amounts (1 ng to 1 µg). RiboCop HMR V2 efficiently reduces rRNA reads to below 1% (Fig. 1) while maintaining unbiased transcript abundance (Fig. 2).

Fig_01 - RiboCop HMR V2

Figure 1 | RiboCop rRNA Depletion for Human/Mouse/Rat efficiently removes rRNA across a wide range of input amounts. NGS libraries were prepared using Lexogen’s CORALL Total RNA-Seq Library Prep Kit. Successful depletion was monitored by sequencing (NextSeq500, 1×75 bp) and subsequent analysis of remaining rRNA reads from untreated (Total RNA) and depleted UHRR (1, 100 ng, and 1 µg). The percentage of reads mapping to rRNA is plotted in blue.

Fig_02 - RiboCop HMR V2

Figure 2 | RiboCop maintains unbiased expression profiles while efficiently removing undesired ribosomal RNA from UHRR. Correlation of transcript abundance in untreated samples vs. samples depleted with RiboCop for Human/Mouse/Rat (HMR) V2 for 1 ng – 1 µg UHRR. Libraries were prepared and sequenced as described in Figure 1. Reads were mapped against the GRCh38.95 reference genome using STAR aligner and counted with FeatureCounts (including multi mappers).

RiboCop enriches RNAs of interest across a wide range of total RNA input amounts from human, mouse, and rat samples (Fig. 3), and shows excellent reproducibility between replicates (Fig. 4).

 
Fig_03 - RiboCop HMR V2

Figure 3 | RiboCop rRNA Depletion for Human/Mouse/Rat (HMR) V2 removes rRNA from human (UHR), mouse (liver), and rat (liver). Two RNA input amounts of the indicated species were depleted with RiboCop HMR V2. Library preparation and sequencing were performed as described in Figure 1. Reads were mapped against the respective reference genomes for human (GRCh38.95), mouse (mmu_GRCm38.95), and rat (rno_Rnor_6.0.95). The percentage of reads mapping to rRNA is plotted in blue.

Fig_04 - RiboCop HMR V2

Figure 4 | Excellent reproducibility between replicates. Correlation of replicates for two independent depletion reactions using 1 ng, 100 ng, and 1 µg total UHRR as input. Total RNA was ribo-depleted with RiboCop HMR V2. Library preparation, sequencing, and data analysis were performed as described in Figure 2. Reads were mapped against the GRCh38.95 reference genome.

RiboCop protocols are robust and highly reproducible. Correlation plots show consistent results over a broad range of inputs (Fig. 5). Additionally, Figure 2 shows a high correlation between transcript abundance in untreated vs. ribo-depleted samples for a wide input range (1 ng to 1 µg) indicating that depletion with RiboCop HMR V2 does not affect the abundance of non-targeted transcripts.

Figure 5 | RiboCop HMR V2 maintains constant transcript abundance across various input amounts. Correlation of transcript abundance in samples depleted with RiboCop HMR V2 for 100 ng RNA vs. 1 ng RNA input for human (UHRR), mouse (mouse liver RNA), and rat (rat liver RNA) samples. Library preparation, sequencing, and data analysis were performed as described in Figure 2. Reads were mapped against the respective reference genomes for human (GRCh38.95), mouse (mmu_GRCm38.95), and rat (rno_Rnor_6.0.95), respectively.

Workflow

Samples are treated using a set of affinity probes for specific depletion of rRNA sequences. RiboCop probes efficiently remove rRNA and therefore afford a comprehensive view of transcriptome composition.

Step1:
Total time:
1 hr 30 min
Hands-on time:
30 min

Affinity probes and total RNA are mixed and denatured.

Denatured total RNA and probes are hybridized.

Depletion beads are conditioned and used to remove probes along with hybridized ribosomal RNA from solution.

The depleted RNA is purified for downstream processing.

Testimonial

“I am pleased with the rRNA depletion using RiboCop – it seems to preserve longer RNAs than an RNase H-based kit tested in direct comparison. Based on this, I chose RiboCop for my large project, and I have recommended the kit to my colleagues.”

Benjamin Fair, PhD, Postdoctoral Researcher, Section of Genetic Medicine, University of Chicago

FAQ

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Downloads

Safety Data Sheet

If you need more information about our products, please contact us through support@lexogen.com or directly under +43 1 345 1212-41.

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