Targeted RNA sequencing

Focus on sequencing specific transcripts of interest to study gene expression and gene fusions in RNA samples

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.

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

RNA sequencing methods guide cover. Close up image of a female scientist pipetting clear liquid into tube; NextSeq 1000/2000 reagent cartridge and sample plate on the lab bench.

RNA sequencing methods guide

This guide provides solutions for profiling RNA, from targeted panels to the whole transcriptome. Illumina RNA-Seq workflows integrate library prep, sequencing, and data analysis to support transcriptome research.

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

Female scientist holding a single pipette in one hand and a tube in the other.

Library prep for RNA-Seq

Our enhanced RNA-Seq library prep portfolio includes removal of abundant rRNA, so you can focus on high-value portions of the transcriptome.

Learn more about RNA library prep

A fast, easy workflow for identifying RNA fusion events for cancer research

Learn how cancer researchers can use Illumina RNA Prep with Enrichment and Trusight panels to get focused results for cancer-related gene expression and fusion detection.

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Targeted RNA-Seq workflow

Illumina offers targeted RNA sequencing workflows that simplify the entire process, from library preparation to data analysis and biological interpretation.

1
Library prep
2
Sequencing
3
Data analysis & insights

Featured RNA-Seq articles

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

Additional resources

Customized panel content to fit your study needs

Illumina Custom Enrichment Panel v2 enables the creation of complete custom or spike-in panels. Enjoy rapid delivery, high on-target enrichment, and a streamlined workflow for efficient and reliable results.

RNA-Seq data analysis

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

FFPE RNA-Seq tips

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

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.

Speak to a specialist

Talk to an expert to learn more about mRNA-Seq solutions.