mRNA Sequencing

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. 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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Advantages of mRNA Sequencing

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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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.

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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Explore the NextSeq 1000 & 2000 Systems

With over 75 breakthrough innovations, these sequencing systems offer dry instrumentation, easier run setup, and fast secondary analysis with DRAGEN software onboard. Experience our simplest workflows yet, and perform a broad range of emerging and mid-throughput sequencing applications.

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Featured mRNA Sequencing Articles

Mapping Neural Diversity
Mapping Neural Diversity

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

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Single-Cell Analysis in Developmental Biology
Single-Cell Analysis in Developmental Biology

Dr. Colin Trapnell discusses his lab's experience with single-cell mRNA-Seq and his efforts to make bioinformatics tools available to all.

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RNA-Seq Considerations
RNA Sequencing Considerations

Learn about read length and depth requirements for RNA-Seq and find resources to help with experimental design.

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Library Prep for RNA Sequencing

mRNA Sequencing Library Prep

Quantify gene expression, identify known and novel isoforms in the coding transcriptome, detect gene fusions, and measure allele-specific expression with our enhanced RNA-Seq library prep solutions.

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Comprehensive mRNA-Seq Workflow

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.

Related Solutions

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.

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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Additional Resources

Methods 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.

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.

RNA-Seq Data Analysis
RNA-Seq Data Analysis

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

NextSeq 1000 and NextSeq 2000 single-cell RNA sequencing solution
NextSeq 1000 and NextSeq 2000 single-cell RNA sequencing 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.

RNA-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.

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.

  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