mRNA sequencing

Detect both known and novel transcripts, measure transcript abundance, and get a comprehensive view of the coding transcriptome

Front view of a female scientist pipetting clear liquid into tube; reagent cartridge, box, and plates in the foreground; NextSeq 1000/2000 instruments in the background.

Introduction to mRNA sequencing

mRNA sequencing (mRNA-Seq) has rapidly become the method of choice for analyzing the transcriptomes of disease states, of biological processes, and across a wide range of study designs. In addition to being a highly sensitive and accurate means of quantifying gene expression, mRNA-Seq can identify both known and novel transcript isoforms, gene fusions, and other features as well as allele-specific expression. Next-generation sequencing (NGS)-based mRNA-Seq delivers a comprehensive view of the coding transcriptome that is not restricted by the filter of prior knowledge.

Advantages of mRNA sequencing

mRNA-Seq provides a number of advantages for analyzing the transcriptome.

Offers a broad dynamic range, enabling sensitive and accurate measurement of fold changes in gene expression

Captures both known and novel transcript features

Can be applied across a wide range of species

Accurate, high-resolution view of the transcriptome

Ratio compression is an established technical limitation of gene expression arrays that reduces dynamic range and can mask or alter measured transcriptional changes.1–3 In contrast, mRNA-Seq is not subject to this bias and provides more comprehensive and accurate measurements of gene expression changes.

Additionally, mRNA-Seq can provide strand information, which enables the detection of antisense expression, allows more accurate quantification of overlapping transcripts, and increases the percentage of alignable reads.

Featured mRNA-Seq workflow

1
Library 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.

2
Sequencing

NextSeq 1000 & 2000 Systems

These cost-efficient, user-friendly, mid-throughput benchtop sequencers support mRNA-Seq plus a wide variety of other current and emerging applications.

MiSeq i100 Series

Our fastest, simplest benchtop system for mRNA sequencing.

3
Data analysis

DRAGEN RNA

Performs alignment, quantification, and fusion detection.

DRAGEN Differential Expression

Enables differential gene expression analysis.

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.

RNA library preparation

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

Learn more about RNA library prep
Female scientist holding a single pipette in one hand and a tube in the other.

Comprehensive mRNA-Seq workflow

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

1
Library prep
2
Sequencing
3
Data analysis, storage, & insights

Featured mRNA sequencing articles

Mapping neural diversity

Allen Institute researchers use mRNA-Seq to analyze gene expression in individual neurons and classify V1 neural cells.

Related content

RNA-Seq in cancer research

Monitoring gene expression changes with mRNA-Seq can help researchers identify biomarkers predictive of disease prognosis or response to therapy.

Learn more about cancer RNA-Seq

Gene expression analysis for disease studies

RNA-Seq-based gene expression profiling studies can provide visibility into how genetic and environmental factors contribute to a broad range of diseases.

Learn more about gene expression profiling

Drug discovery and development

Explore innovative genomics and multiomics solutions designed to accelerate drug discovery and development.

Learn more about drug discovery

Additional resources

RNA-Seq data analysis

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

Single-cell RNA sequencing

Study cellular differences often masked by bulk sampling and explore highly sensitive single-cell sequencing methods.

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.

References

  1. Shi L, Tong W, Su Z, et al. Microarray scanner calibration curves: characteristics and implications. BMC Bioinformatics. 2005;6 Suppl 2:S11.
  2. Naef F, Socci ND, Magnasco M. A study of accuracy and precisions in oligonucleotide arrays: extracting more signal at large concentrations. Bioinformatics. 2003;19:178-184.
  3. Yuen T, Wurmbach E, Pfeffer RL, Ebersole BJ, Sealfon SC. Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucleic Acids Res. 2002;30:e48.