RNA Sequencing

Introduction to RNA Sequencing

RNA sequencing (RNA-Seq) is revolutionizing the study of the transcriptome. A highly sensitive and accurate tool for measuring expression across the transcriptome, it is providing scientists with visibility into previously undetected changes occurring in disease states, in response to therapeutics, under different environmental conditions, and across a wide range of other study designs.

RNA-Seq allows researchers to detect both known and novel features in a single assay, enabling the identification of transcript isoforms, gene fusions, single nucleotide variants, and other features without the limitation of prior knowledge.1,2

childern near a lake at sunset - RNA-Seq is transforming the world around us
Propelling Progress with RNA-Seq

RNA sequencing can have far-reaching effects on research and innovation, transforming our understanding of the world around us.

Benefits of RNA Sequencing

RNA-Seq with next-generation sequencing (NGS) is increasingly the method of choice for scientists studying the transcriptome.

  • Covers an extremely broad dynamic range
  • Provides sensitive, accurate measurement of gene expression
  • Captures both known and novel features; does not require predesigned probes
  • Generates both qualitative and quantitative data
  • Reveals the full transcriptome, not just a few selected transcripts
  • Can be applied to any species, even if a reference sequence is not available
RNA Sequencing Empowers Transcriptomics

Learn how RNA-Seq is advancing transcriptome research in various fields, and how gene regulation studies can provide complementary information.

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RNA Sequencing Publication Review

RNA-Seq is by far the most cited NGS method. This collection contains protocol diagrams, advantages and disadvantages, and related peer-reviewed publications on various RNA-Seq methods featuring Illumina technology.

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RNA Sequencing Publication Review
learn about Illumina NGS technology
New To NGS?

Find out how Illumina NGS technology works and what types of experiments it enables.

learn about NGS RNA analysis
How Can I Use NGS to Analyze RNA?

Learn about key RNA-Seq methods. Find out how they differ to help you determine the method most appropriate for your research.

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learn how to apply RNA-Seq
How Can I Apply RNA-Seq?

Study gene expression and transcriptome changes with cancer RNA-Seq.

Analyze pathogen transcriptome signatures with microbial RNA-Seq.

Study drug response RNA biomarkers.

Frequently Purchased Together

Featured RNA Sequencing Articles

Precision Immunotherapies Using Tumor-Specific HLA Ligands
Precision Immunotherapies Using Tumor-Specific HLA Ligands

RNA-Seq and HLA typing are increasing the power and efficiency of a target discovery platform.

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The Time Is Now for Microbiome Studies
The Time Is Now for Microbiome Studies

Transcriptomics and whole-genome shotgun sequencing provide researchers and pharmaceutical companies with data to refine drug discovery and development.

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Circulating RNA
Cell-Free RNA as a Noninvasive Biomarker

This research highlights the broad potential of circulating cell-free RNA sequencing for biomarker discovery and noninvasive health monitoring.

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Library Prep for RNA Sequencing

Library Prep for RNA Sequencing

Advances in RNA-Seq library prep are revolutionizing the study of the transcriptome. Our enhanced RNA-Seq library prep portfolio spans multiple types of sequencing studies. These solutions offer rapid turnaround time, broad study flexibility, and sequencing scalability.

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Experimental Considerations for RNA-Seq

Plan Your RNA-Seq Experiments

Featured Products

Illumina Stranded mRNA Prep
Illumina Stranded mRNA Prep

A simple, scalable, cost-effective, rapid single-day solution for analyzing the coding transcriptome leveraging as little as 25 ng input of standard (non-degraded) RNA.

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NextSeq 1000 & 2000 Systems

These cost-efficient, user-friendly, mid-throughput benchtop sequencers offer extreme flexibility to support new and emerging applications.

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Performs alignment, quantification, and fusion detection.

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RNA-Seq Differential Expression
RNA-Seq Differential Expression

Enables differential gene expression analysis.

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Yes, RNA-Seq is a well-established and accepted method for quantifying gene expression. To see how RNA-Seq compares against microarrays and quantitative PCR (qPCR), view the pages below:

Transcriptomics broadly refers to the study of RNA related to its expression levels, function, structure, and regulation. RNA-Seq is more specific and refers to the technique to study both the sequence and quantity of RNA.

RNA sequencing depth is the ratio of the total number of bases obtained by sequencing to the size of the genome or the average number of times each base is measured in the genome.

Bulk RNA-Seq is a method that analyzes pooled RNA from cells or tissues.

RNA sequencing strandedness allows researchers to determine which DNA strand (sense or antisense) a transcript came from. Compared to regular RNA sequencing methods, stranded RNA sequencing can find novel transcripts, distinguish transcripts from overlapping genes, find antisense sequences, and annotate genes.

Visit the Illumina Stranded mRNA Prep page for more information.

In mRNA library preparation methods, mRNA is selected via oligodT beads from total RNA, so libraries are prepared only from polyadenylated transcripts from samples. In total RNA workflows, rRNA and select other abundant transcripts are depleted from samples, and the remaining RNAs are prepared into sequencing libraries, including polyadenylated and non-polyadenylated RNAs. In enrichment workflows, libraries are prepared from all RNA samples. These libraries are subsequently enriched using an oligo probe panel. Panels can target full coding exomes, transcripts associated with specific diseases, RNA from pathogens, or custom targets. For more information on these workflows, visit the following pages:

Extracted RNA must be purified and free of contaminants. Illumina recommends following the guidelines provided in your particular RNA isolation kit and selecting an appropriate protocol for your sample type.

The following provides input ranges of RNA for your selected method:

RNA-Seq is compatible with all Illumina sequencers. Depending on the library preparation kit, the application, and the data needs, higher or lower throughput sequencers may be more appropriate.

Explore all Illumina sequencing platforms

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Yes, RNA-Seq library preparation methods can be automated. Visit our Library Prep Automation page for more information.

Yes, Illumina offers quality control solutions depending on your application. See our library quantification and QC reference guide for detailed information.

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Additional Resources

Workflows for RNA Sequencing Guide
Workflows for RNA Sequencing Guide

Learn about Illumina solutions for next-generation RNA sequencing applications.

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RNA-Seq of Low-Quality and FFPE Samples

RNA-Seq of formalin-fixed, paraffin-embedded (FFPE) and other low-quality samples offers valuable insights for disease research.

Gene Target Identification

Uncover gene targets and pathways tied to disease.

RNA-Seq Data Analysis

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

COVID-19 Host Risk and Response
COVID-19 Host Risk and Response

Identify genetic variants linked to COVID-19 disease severity and profile the immune response to SARS-CoV-2 with NGS and microarrays.

Unlock a New Spatial View of Multicellular Tissues
Unlock a New Spatial View of Multicellular Tissues

Visualize tissue morphology overlaid with gene activity, to reveal the spatial relationships between cells and how they contribute to tissue development, function, and disease state.

NextSeq 1000 and NextSeq 2000 single-cell RNA sequencing solution pdf
NextSeq 1000 and 2000 single-cell RNA-Seq solution

This cost-effective, flexible workflow measures gene expression in single cells and offers high-resolution analysis to discover cellular differences usually masked by bulk sampling methods.

  1. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10:57–63.
  2. Wilhelm BT, Landry JR. RNA-Seq—quantitative measurement of expression through massively parallel RNA sequencing. Methods. 2009;48:249–57.