Targeted RNA Sequencing

Introduction to Targeted RNA Sequencing

Targeted RNA-sequencing (RNA-Seq) is a highly accurate method for selecting and sequencing specific transcripts of interest. It offers both quantitative and qualitative information. Targeted RNA-Seq can be achieved via either enrichment or amplicon-based approaches, both of which enable gene expression analysis in a focused set of genes of interest. Enrichment assays also provide the ability to detect both known and novel gene fusion partners in many sample types, including formalin-fixed paraffin-embedded (FFPE) tissue.

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Advantages of Targeted Enrichment RNA-Seq

RNA enrichment provides quantitative expression information as well as the detection of small variants and gene fusions. RNA enrichment offers the following features:

  • Compatible with difficult samples such as FFPE tissue
  • Low input (requires 10 ng of total RNA or 20 – 100 ng of FFPE RNA)
  • Detects both known and novel fusion gene partners
  • Profiles gene expression with a broad dynamic range

Advantages of Targeted Amplicon RNA-Seq

RNA expression panels can be designed to focus on RNA sequences of interest, or custom content can be added to fully optimized and experimentally validated panels.

  • Offers a highly accurate and specific method for measuring transcripts of interest
  • Provides qualitative and quantitative information for differential expression analysis, allele-specific expression measurement, and gene fusion verification
  • Measures dozens to thousands of targets simultaneously
  • Is compatible with low-quality or FFPE-derived RNA samples
New Views of Cancer Pathways in Pediatric Leukemia

Researchers are using the TruSight RNA Pan-Cancer Panel to understand the role of fusion genes in pediatric leukemia.

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Library Prep for RNA Sequencing

RNA Sequencing Library Prep

Our RNA-Seq library prep solutions for targeted RNA sequencing include exceptionally fast, tagmentation-based workflows for deep insights into many transcripts of interest, including the RNA exome.

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RNA Sequencing Considerations

Each RNA-Seq experiment type—whether it’s gene expression profiling, targeted RNA expression, or small RNA analysis—has unique requirements for read length and depth. This bulletin reviews experimental considerations and offers resources to help with study design.

Illumina Knowledge
RNA Sequencing Considerations

Targeted RNA-Seq Workflow

Illumina sequencing by synthesis (SBS) chemistry is the most widely adopted NGS technology, generating approximately 90% of global sequencing data.*

We offer integrated targeted RNA-Seq workflows that simplify the entire process, from library preparation to data analysis and biological interpretation.

Gene Panel and Array Finder

Identify sequencing panels or microarrays that target your genes of interest. Search panels by gene, or find genotyping arrays by genomic location, variant ID, or species.

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Gene Panel and Array Finder

Related Solutions

Cancer Research: Variant Detection

Monitor gene expression and transcriptome changes with targeted RNA-Seq to better understand which variants are expressed and which may affect tumorigenesis and progression. Learn more about RNA-Seq in cancer research.

Drug Development Research

Explore genomic sequencing solutions for all phases of the drug development pipeline. Characterize gene expression profiles from a custom panel with a few defined targets to the whole transcriptome. Learn more about NGS in drug development.

Neurogenomics Research

Genomic technologies can help reveal the mechanisms behind complex neurological diseases such as Alzheimer’s and Parkinson's disease. Learn more about neurogenomics.

Immunogenomics Research

See how NGS enables research into autoimmune disease mechanisms, the immune repertoire, and the functional consequences of immune-related genetic variation. Learn more about immunogenomics.

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Additional Resources

RNA-Seq Methods Review
RNA-Seq Methods Review

This overview discusses recent RNA-Seq research publications featuring Illumina technology.

Push-Button Informatics
Push-Button Informatics

Illumina bioinformatics tools make it easier to manage, analyze, and interpret large amounts of complex genomic data.

Targeted RNA-Seq and Circadian Rhythms
Targeted RNA-Seq and Circadian Rhythms

Dr. Hughes at University of Missouri-St. Louis uses targeted RNA-Seq to uncover the genetic mechanisms of circadian rhythms.


RNA-Seq analysis of FFPE and other low-quality samples offers valuable insights for disease research.

RNA-Seq Data Analysis
RNA-Seq Data Analysis

User-friendly software tools simplify RNA-Seq data analysis for biologists, regardless of bioinformatics experience.

Paired-End RNA-Seq
Paired-End RNA-Seq

All Illumina sequencing systems are capable of paired-end sequencing, which facilitates detection of novel RNA transcripts, gene fusions, and more.

*Data calculations on file. Illumina, Inc., 2015