KAPA RNA HyperPrep Kits

For Research Use Only. Not for use in diagnostic procedures.

Overview

RNA library preparation is the critical first step of RNA sequencing (RNA-seq) and KAPA RNA HyperPrep kits offers flexible workflow options with streamlined single-tube single-day workflows that include enrichment of desired transcripts by selective mRNA capture or rRNA depletion. These kits have been optimized for high performance even with degraded and low-input samples, and offer the option of custom RNA depletion. KAPA RNA HyperPrep Kits contain high-quality enzymes, including KAPA HiFi DNA polymerase, developed through our Directed Evolution Technology for constructing RNA libraries with minimal GC bias and even sequence coverage.

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Introducing a shorter and more streamlined RNA-seq workflow

This new, optimized workflow for KAPA RNA HyperPrep with RiboErase (HMR) saves over an hour compared to the standard workflow, and as much as 3 hours compared to kits from other suppliers. With this new protocol, the total turnaround time— including ribodepletion— is about 5 hours.

Download the Tech Spotlight to learn more, and contact us for the protocol.

Benefits of KAPA RNA HyperPrep Kits

Thinking of automating library prep on your existing liquid handler?

Roche’s NGS Automation Support Team, in collaboration with non-Roche liquid handling vendors, creates menus of automated methods for KAPA library prep reagents.

Let’s talk about the next steps to get you up and running with automating your NGS library prep protocols. Visit support for non-Roche liquid handlers to learn more.

KAPA RNA HyperPrep Kits compared to 2 suppliers

Depletion of rRNA, user-defined RNA, and globin transcript.

Whole-transcriptome sequencing provides a complete view of the transcriptome, including immature and noncoding RNAs. In these workflows, it is important to remove rRNA (up to 95% of the total RNA sample) prior to library prep in order to minimize the number of wasted sequencing reads. This method is effective with degraded RNA inputs not suitable for mRNA capture. Enzymatic depletion can also be used to remove other transcripts, such as globin mRNA and/or other highly abundant RNAs.

mRNA Capture

mRNA capture sequencing is used for the analysis of coding transcripts in eukaryotic samples, allowing researchers to detect and quantify relative expression levels. This workflow enriches for mRNA over non-polyadenylated species such as ribosomal, precursor, and non-coding RNAs.

KAPA RNA HyperPrep Kits provide streamlined and strand-specific library construction.

The novel chemistry employed in KAPA RNA HyperPrep Kits allows for fewer and shorter enzymatic steps, reducing hands-on time and overall library prep time. rRNA depletion with KAPA RiboErase (HMR) or KAPA RiboErase (HMR) Globin Kits adds approximately 2.5 hours to the overall workflow time, whereas mRNA capture adds approximately 1.5 hours. The entire workflow, from input RNA to sequencing-ready library, can easily be completed in a standard workday. All KAPA RNA HyperPrep library construction workflows are automation friendly.

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KAPA RNA HyperPrep Kits Specifications and Comparison

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Product Name	KAPA RNA HyperPrep Kits	KAPA mRNA HyperPrep Kits	KAPA RNA HyperPrep Kits with RiboErase (HMR)	KAPA RNA HyperPrep Kits with RiboErase (HMR) Globin
Library Preparation Duration	4 hours	5.5 hours	6.5 hours	6.5 hours
Sample Input Amount	1-100 ng into library prep	50 ng - 1 µg into mRNA capture	25 ng - 1 µg into rRNA depletion	25 ng - 1 µg into rRNA depletion
Sample Types	High-quality total RNA Degraded or FFPE total RNA Poly(A)-selected and/or depleted RNA	High-quality total RNA	High-quality total RNA Degraded or FFPE total RNA	High-quality total RNA Degraded or FFPE total RNA Whole blood total RNA
Species	Eukaryotic (Animal, Plant, etc.) Prokaryotic (Bacteria, etc.) Viral	Eukaryotic (Animal, Plant, etc.)	Human, Mouse, and Rat Other species can be supported via custom rRNA depletion	Human, Mouse, and Rat Other species can be supported via custom rRNA depletion
Stranded RNA-sequencing	Yes	Yes	Yes	Yes
Amplification	KAPA HiFi DNA Polymerase Compatible with low bias amplification	KAPA HiFi DNA Polymerase Compatible with low bias amplification	KAPA HiFi DNA Polymerase Compatible with low bias amplification	KAPA HiFi DNA Polymerase Compatible with low bias amplification
Reaction Purification	KAPA Pure Beads included	KAPA Pure Beads included	KAPA Pure Beads included	KAPA Pure Beads included
Multiplexing	Yes. KAPA Adapters are not supplied, but available separately	Yes. KAPA Adapters are not supplied, but available separately	Yes. KAPA Adapters are not supplied, but available separately	Yes. KAPA Adapters are not supplied, but available separately
Applications	Whole-transcriptome sequencing Gene expression with target enrichment Splice junction and gene fusions with target enrichment	Gene expression Annotation Splice junction and gene fusions	Whole-transcriptome Long non-coding RNA Annotation Gene expression Splice junction and gene fusions	Whole-transcriptome Long non-coding RNA Annotation Gene expression Splice junction and gene fusions
Automation Friendly	Yes. Demonstrated and verified on many liquid handling systems. Learn more	Yes. Demonstrated and verified on many liquid handling systems. Learn more	Yes. Demonstrated and verified on many liquid handling systems. Learn more	Yes. Demonstrated and verified on many liquid handling systems. Learn more
Compatible Sequencing Platforms	Illumina Sequencers	Illumina Sequencers	Illumina Sequencers	Illumina Sequencers
Storage Information	Enzymes and buffers can be stored for up to 10 months at -20°C KAPA Pure Beads can be stored for up to 10 months at 4°C	Enzymes and buffers can be stored for up to 10 months at -20°C KAPA Pure Beads can be stored for up to 10 months at 4°C	Enzymes and buffers can be stored for up to 10 months at -20°C KAPA Pure Beads can be stored for up to 10 months at 4°C	Enzymes and buffers can be stored for up to 10 months at -20°C KAPA Pure Beads can be stored for up to 10 months at 4°C

The first-generation KAPA Stranded RNA-seq Kits are still available for purchase. For more information about these older RNA library kits, please click here.

KAPA RNA HyperPrep Kits

These fast, robust RNA library preparation kits can be used with a wide variety of RNA input types, qualities, and amounts. They enable many different workflow options, including ribosomal depletion and mRNA capture for eukaryotic or prokaryotic RNA-seq libraries.

KAPA RNA HyperPrep with RiboErase (HMR)

Includes all reagents for efficient enzymatic depletion of ribosomal RNA (rRNA) from human, mouse, and rat (HMR) samples of high-or low-quality RNA
Provides a more comprehensive view of the whole transcriptome compared to mRNA capture
Can be used for custom depletion of rRNA from other organisms when the HMR oligos are replaced with custom sequences

Efficient rRNA depletion using KAPA RNA HyperPrep with RiboErase (HMR) leads to fewer non-informative reads and the detection of more unique transcripts compared to other suppliers.

Libraries were generated in quadruplicate using variable inputs of Universal Human Reference (UHR) RNA (Agilent Technologies) with rRNA de[pletion prior to library construction. Where present, error bars represent the standard deviation. For 25 ng samples, paired end (2 x 100 bp) sequencing was performed using an Illumina® HiSeq® 2500 instrument. Reads aligning to rRNA were removed, and reads were randomly subsampled to 14 M for comparative analyses. Transcripts were quantified using RNA-SeQC. The 10 ng input amount is lower than the validated minimum input for both KAPA RNA HyperPrep workflows; for these samples, paired-end (2 x 75 bp) sequencing was performed using an Illumina NextSeq 500 instrument. Reads were randomly subsampled to 14 M for comparative analysis prior to removing reads aligning to rRNA and subsequent marking of duplicates. Transcripts were quantified using Kallisto (data not plotted due to analysis and sequencing depth differences).

KAPA RNA HyperPrep with RiboErase (HMR) Globin

Includes all reagents for efficient enzymatic depletion of globin mRNA from blood-derived RNA samples from high- or low-quality RNA
Includes reagents for the depletion of human, mouse, or rat (HMR) rRNA

KAPA RNA HyperPrep Kit with RiboErase (HMR) Globin simultaneously removes rRNA and globin mRNA from blood-derived RNA. Together, effective RNAase H depletion and highly efficient library construction result in fewer non-informative reads

(A) compared to the workflow from Supplier I, which employs bead-based depletion (orange). This translates to more complex libraries (B) and a larger number of unique transcripts detected (C).

Libraries were prepared from different inputs of RNA extracted from human blood, as indicated on the x-axis of each graph. The 25 ng input is lower than the recommended minimum input for the Supplier I workflow. Paired-end (2 x 125 bp) sequencing was performed on an Illumina® HiSeq® 2500 instrument. Data were sub-sampled to 17 M reads per sample for analysis. Each bar represents the average of three technical replicates. Transcript abundance was quantified using Kallisto. To assess off-target depletion, transcript abundances were aggregated at the gene level and TMM-normalized prior to differential expression analysis. The expression profiles of libraries generated with or without globin depletion were compared to assess off-target depletion for each workflow.

KAPA mRNA HyperPrep Kit

Includes reagents for the enrichment of eukaryotic mRNA from high-quality total RNA
Provides a focused view of the protein-coding regions of the transcriptome

Efficient mRNA capture using KAPA mRNA HyperPrep leads to fewer non-informative reads and the detection of more unique transcripts compared to other suppliers.

Libraries were generated in quadruplicate using variable inputs of Universal Human Reference (UHR) RNA (Agilent Technologies) with mRNA capture prior to library construction. For 50 ng samples, paired end (2 x 100 bp) sequencing was performed using an Illumina® HiSeq® 2500 instrument. Reads aligning to rRNA were removed, and reads were randomly subsampled to 14 M for comparative analyses. Transcripts were quantified using RNA-SeQC. The 10 ng input amount is lower than the validated minimum input for both KAPA RNA HyperPrep workflows; for these samples, paired-end (2 x 75 bp) sequencing was performed using an Illumina NextSeq 500 instrument. Reads were randomly subsampled to 14 M for comparative analysis prior to removing reads aligning to rRNA and subsequent marking of duplicates. Transcripts were quantified using Kallisto (data not plotted due to analysis and sequencing depth differences).

Videos

A Shorter Protocol for KAPA RiboErase and RNA HyperPrep

Introducing a shorter, more streamlined RNA-seq workflow.

Watch the video to learn more, and contact us for the protocol.

Importance of performing ribosomal RNA depletion

In this short video (~3 min), you’ll learn how the depletion of ribosomal RNA (rRNA) can improve your RNA-seq results. You’ll also learn about the differences between enzymatic and bead-based methods, and how these methods can be modified to enable custom depletion of user-defined transcripts. Presented by Nicholas Hapshe, Roche Sequencing and Life Science.

What is Stranded RNA Sequencing?

What is stranded RNA sequencing, and how is it different from other RNA-seq workflows? This video describes the library preparation workflow for stranded RNA-seq, and explains the benefits of using this method. These include the ability to separately identify transcripts originating from each DNA strand, increasing the accuracy of RNA-seq data and providing additional insights-- especially important when genes on opposite strands overlap.

Presented by Dustin Masser, Roche Sequencing and Life Science

Webinars

RNA:Seq: Addressing the Challenges using KAPA RNA HyperPrep

RNA-sequencing (RNA-seq) and the study of transcriptomes have become essential in both molecular and clinical research. Many researchers and sequencing service providers have found RNA-seq difficult to adopt due to various challenges.

In this webinar, we discuss:

What RNA-seq is and why it is crucial in research
Unique RNA-seq challenges in sample handling, library preparation, and data analysis
KAPA RNA HyperPrep workflows and how they can help overcome these challenges
Q&A with an experienced Roche field application specialist

Presented by Drew Cheney, Field Applications Scientist, Roche Sequencing and Life Science

Automating RNA-seq Library Preparation

Automating RNA-sequencing (RNA-seq) library preparation offers advantages such as higher sample throughput, less hands-on time, fewer human errors, greater reproducibility, and better process control and workflow standardization. However, developing and implementing an automated RNA-seq library prep protocol on a liquid handling platform can be challenging and time-consuming.

In this webinar, we discuss the automation of RNA-seq library prep, including:

Benefits of automating RNA-seq library prep
Tips and tricks of NGS automation
Overview of the Roche Sequencing automation program
Examples of automated workflows for KAPA RNA HyperPrep

RNA-seq Applications for SARS-CoV-2 Research

In this presentation, you’ll learn about high-throughput SARS-CoV-2 research using RNA-seq. Highlighted methods include whole-transcriptome and target-enriched sequencing, using both hybridization-based and amplicon workflows. Presented by Sarah Trusiak, Senior Applications Scientist at Roche Sequencing and Life Science on August 28, 2020.

Ultra-low input and single-cell mRNA-seq library prep using KAPA HyperPlus Kit

Understanding the cellular heterogeneity of tissues such as tumors is crucial for both translational and clinical research. As a result, highly focused techniques such as single-cell RNA sequencing (scRNA-seq) and ultra-low-input mRNA-seq are expanding rapidly to overcome the challenges that single cells and restricted cell populations pose for library preparation and reliable transcriptome analysis.

In many scRNA-seq workflows, the initial steps employ the template switching method for cDNA synthesis followed by cDNA normalization prior to library preparation. Roche’s KAPA HyperPrep Kit is effective across a 30-fold range of cDNA input amounts, eliminating the need for cDNA normalization in scRNA-seq workflows while also generating complex, uniform libraries and high-quality sequencing data.

In this webinar, we:

Present an ultra-low-input workflow that yields high-quality libraries from as little as 10 pg of input RNA using the template switching method for cDNA synthesis followed by library preparation using KAPA HyperPlus Kit
Demonstrate the advantages of the KAPA HyperPlus Kit over the tagmentation-based methods, including greater flexibility on cDNA input quantities
Present scRNA data from libraries prepared with KAPA HyperPlus Kit

Presented by Mariana Fitarelli Kiehl, PhD, Senior Applications Scientist at Roche Sequencing and Life Science

Ordering

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KAPA Cat. No	Roche Cat. No	Description	Kit Size
KK8560	08098131702	KAPA RNA HyperPrep with RiboErase (HMR)	24 libraries
KK8561	08098140702	KAPA RNA HyperPrep with RiboErase (HMR)	96 libraries
KK8540	08098093702	KAPA RNA HyperPrep Kit	24 libraries
KK8541	08098107702	KAPA RNA HyperPrep Kit	96 libraries
KK8580	08098115702	KAPA mRNA HyperPrep Kit	24 libraries
KK8581	08098123702	KAPA mRNA HyperPrep Kit	96 libraries
KK8562	08308314702	KAPA RNA HyperPrep Kit with RiboErase (HMR) Globin	24 libraries
KK8563	08308241702	KAPA RNA HyperPrep Kit with RiboErase (HMR) Globin	96 libraries

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KAPA Cat. No	Roche Cat. No	Description	Kit Size
KK8721	08278539001	KAPA Adapter Dilution Buffer (25 mL)	25 mL
KK8727*	08861919702	KAPA Unique Dual-Indexed Adapter Kit, (15 µM)	96 adapters x 20 µl each

*Contains KAPA Adapter Dilution Buffer, as well as three additional sealing films to support multiple use

KAPA RNA HyperPrep Kits

KAPA RNA HyperPrep Kits Specifications and Comparison

KAPA RNA HyperPrep Kits Specifications and Comparison

KAPA RNA HyperPrep Kits

Brochures

App Notes

Peer-Reviewed Publications

Videos

Webinars

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