RNA-sequencing (RNA-seq)

A powerful technique for transcriptome research

Banner with title RNA-sequencing (RNA-seq), gene expression

What is RNA-seq?

RNA-sequencing (RNA-seq) is a powerful method for studying the transcriptome—the entire spectrum of coding and noncoding RNA transcripts present in a cell or tissue. The transcriptome can provide valuable insights into cellular behavior at a particular moment, whether at rest or when responding to changes in the environment, therapeutic treatments, or developmental progression. RNA-seq also enables the identification of variant splicing events, novel transcripts, mutations, gene fusions, isoforms, and single nucleotide variants (SNVs).

RNA-seq strategies and workflows

The best RNA-seq workflow for your experiment depends on the questions you are trying to answer, the quality of the RNA sample, the amount of RNA available, and the nature of the transcripts of interest. The KAPA RNA HyperPrep Kit  is a robust, streamlined library preparation solution for the preparation of total RNA libraries, and forms the basis for KAPA RNA-seq workflows for transcriptome sequencing with ribodepletion, custom depletion, and mRNA capture workflows (see below).

 

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

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 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. 

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RNA-seq library prep is the critical first step

Roche’s 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.

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Explore custom probe design for rRNA depletion

KAPA RiboDesigner is Roche’s new custom probe design tool for depletion of custom rRNA targets. This algorithm selects non-redundant probe sequences across the target regions, minimizing the total number of probes needed for effective depletion. No bioinformatics expertise is required, and there is no charge for this service.

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Automate RNA-seq library preparation

Automation increases throughput, reduces hands-on time, reduces human error, and enables workflow standardization. It also minimizes potential pipetting errors and standardizes workflows for improved results. Validated scripts are available for KAPA RNA HyperPrep Kits for many liquid handling instruments.

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Genialis

Streamline RNA-seq data analysis for KAPA RNA HyperPrep Kits – no bioinformatics experience required

Managing the enormous amount of RNA-seq data is a challenge, and it can take weeks to receive an analysis report from external bioinformaticians. Roche collaborates with Genialis to offer a biologist-friendly cloud-based analysis application that runs raw sequencing data through preconfigured automated pipelines, tracks how each sample was processed, visualizes and interprets results in real time, and manages all the projects in the cloud.

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RNA-seq Resources