A clear, more complete view of the coding transcriptome

mRNA-Seq detects known and novel transcripts and measures transcript abundance for accurate, comprehensive analysis

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. mRNA-Seq delivers a complete view of the coding transcriptome that is not restricted by the filter of prior knowledge.

mRNA-Seq in 3 Simple Steps

Analyze the coding transcriptome in standard mRNA samples with this seamless workflow solution.

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mRNA-Seq provides a number of advantages over gene expression arrays in analyzing the transcriptome.

  • Offers a broader dynamic range, enabling more sensitive and accurate measurement of fold changes in gene expression
  • Captures both known and novel features
  • Can be applied across a wide range of species


Transitioning from Arrays to mRNA-Seq

Expression Analysis developed tools to make it easier to compare mRNA-Seq results with previous array data.

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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.

Autism and mRNA-Seq

Stanley Lapidus, President, CEO, and Founder, SynapDx, discusses how the company is using mRNA-Seq to study autism.

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

In addition to our industry-leading data quality, Illumina offers integrated mRNA-Seq workflows that simplify the entire process, from library preparation to data analysis and biological interpretation.

Click on the below to view products for each workflow step.

TruSeq Stranded mRNA Library Prep Kit

Streamlined, cost-efficient, and scalable library preparation for mRNA-Seq, with precise measurement of strand orientation. Accurately measure gene and transcript abundance and detect both known and novel features in the coding transcriptome.

TruSeq RNA Exome

Low all-in cost solution for mRNA-seq of low-quality/FFPE samples. Accurately measure gene and transcript abundance and detect both known and novel features in the coding transcriptome.

Find the Right Library Prep Kit

Use this tool to determine the best kit for your needs.

MiSeq System

Speed and simplicity for focused applications, sequencing 1 mRNA sample per run.

NextSeq 550 System

Flexible desktop sequencer supporting multiple applications, enabling 5–16 mRNA samples to be sequenced in a single run.

HiSeq 4000 System

High-throughput RNA-Seq with up to 100 human transcriptomes on the HiSeq 4000 System.

NovaSeq 6000 System

Scalable throughput and flexibility for virtually any genome, sequencing method, and scale of project.

Platform Comparison Tool

Compare sequencing platforms and identify the best system for your lab and applications.

Sequencing Reagents

Find kits that include sequencing reagents, flow cells, and/or buffers tailored to each Illumina sequencing system.

RNA Express App

Aligns RNA-Seq reads with the STAR aligner and assigns aligned reads to genes, followed by differential expression with DESeq2.

TopHat Alignment App

Maps reads, performs abundance estimations of reference genes and transcripts, calls variants, and offers optional fusion calling.

Cufflinks Assembly & Differential Expression (DE) App

Assembles novel transcripts and performs differential expression of novel and reference transcripts.

Integrative Genomics Viewer

A genome browser developed by the Broad Institute of MIT and Harvard that displays NGS data for complex variant analysis.

Illumina DRAGEN Bio-IT Platform

The Illumina DRAGEN (Dynamic Read Analysis for GENomics) Bio-IT Platform provides ultra-rapid secondary analysis of NGS data. A variety of apps are available, including one designed to enable gene fusion studies.

Genomatix Pathway System (GePS)

Associates single gene or list of genes with annotation data for pathways, diseases, tissues, and small molecules.

iPathway Guide

Differential gene expression, drug interaction, and disease analysis.

BaseSpace Sequence Hub

The Illumina genomics computing environment for NGS data analysis and management.

BaseSpace Correlation Engine

A growing library of curated genomic data to support researchers in identifying disease mechanisms, drug targets, and biomarkers.

mRNA-Seq for Cancer Research
mRNA-Seq for 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 Complex Disease Studies
Gene Expression Profiling for Complex Disease Studies

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

RNA Drug Response Biomarker Discovery
RNA Drug Response Biomarker Discovery

Find out how to utilize RNA-Seq to identify novel RNA-based drug response biomarkers. Access resources designed to help new users adopt this application. Learn more about drug response RNA biomarker analysis.

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Illumina NGS Application Guide
Methods Guide

All the information you need, from BeadChips to library prep to sequencer selection and analysis. Use this guide to select the best tools for your lab.

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Single-Cell mRNA-Seq
Single-Cell mRNA-Seq

Dr. Norma Neff discusses how researchers at Stanford University are using single-cell mRNA-Seq to understand early development.

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mRNA-Seq Data Analysis
RNA-Seq Data Analysis

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

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RNA-Seq for Gene Expression Studies
RNA-Seq for Gene Expression Studies

Illumina offers an integrated mRNA-Seq workflow for a deeper understanding of biology.

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mRNA-Seq of Low-Quality and FFPE Samples
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.

Explore FFPE RNA-Seq
Paired-End RNA Sequencing
Paired-End RNA Sequencing

Paired-end RNA-Seq enables discovery applications such as detecting gene fusions and characterizing novel splice isoforms.

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ore Sequencing Lab Benefits from BaseSpace Cloud
Core Sequencing Lab Benefits from BaseSpace Cloud

BRC-Seq uses BaseSpace for sample tracking as well as data analysis, management, and sharing.

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Gene Panel and Array Finder
Gene Panel and Array Finder

Identify sequencing panels or microarrays that target your genes of interest.

Find the Right Product
  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.

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