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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.
Analyze the coding transcriptome in standard mRNA samples with this seamless workflow solution.
mRNA-Seq provides a number of advantages over gene expression arrays in analyzing the transcriptome.
Expression Analysis developed tools to make it easier to compare mRNA-Seq results with previous array data.
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.
Stanley Lapidus, President, CEO, and Founder, SynapDx, discusses how the company is using mRNA-Seq to study autism.
Streamlined, cost-efficient, and scalable library preparation for mRNA-Seq.
Desktop sequencer supporting multiple applications, enabling 5-16 mRNA samples to be sequenced in a single run.
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.
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 Access Library Prep KitLow 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.
Determine the best kit for your needs.
Speed and simplicity for focused applications, sequencing 1 mRNA sample per run.
NextSeq SeriesFlexible desktop sequencer supporting multiple applications, enabling 5–16 mRNA samples to be sequenced in a single run.
HiSeq 2500 SystemPower and efficiency to sequence 12–80 mRNA samples per run.
HiSeq 3000/HiSeq 4000 SystemsHigh-throughput RNA-Seq, with up to 50 or 100 human transcriptomes on the HiSeq 3000 System and HiSeq 4000 System, respectively.
Scalable throughput and flexibility for virtually any genome, sequencing method, and scale of project.
Platform Comparison ToolCompare sequencing platforms and identify the best system for your lab and applications.
Sequencing ReagentsFind kits that include sequencing reagents, flow cells, and/or buffers tailored to each Illumina sequencing system.
Aligns RNA-Seq reads with the STAR aligner and assigns aligned reads to genes, followed by differential expression with DESeq2.
TopHat Alignment AppMaps reads, performs abundance estimations of reference genes and transcripts, calls variants, and offers optional fusion calling.
Cufflinks Assembly & Differential Expression (DE) AppAssembles novel transcripts and performs differential expression of novel and reference transcripts.
The Broad’s IGVA genome browser developed by the Broad Institute of MIT and Harvard that displays NGS data for complex variant analysis.
Associates single gene or list of genes with annotation data for pathways, diseases, tissues, and small molecules.
iPathway GuideDifferential gene expression, drug interaction, and disease analysis.
BaseSpace Sequence HubThe Illumina genomics computing environment for NGS data analysis and management.
BaseSpace Correlation EngineA growing library of curated genomic data to support researchers in identifying disease mechanisms, drug targets, and biomarkers.
Cancers accumulate numerous genetic changes, but typically only a few drive tumor progression. 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 profiling studies provide visibility into how genetic and environmental factors contribute to common disease. RNA-Seq can help identify targets of interest for downstream investigation across a broad range of complex diseases. Learn more about gene expression profiling.
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.
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.
Dr. Norma Neff discusses how researchers at Stanford University are using single-cell mRNA-Seq to understand early development.
User-friendly software tools simplify mRNA-Seq data analysis for biologists, regardless of bioinformatics experience.
Illumina offers an integrated mRNA-Seq workflow for a deeper understanding of biology.
RNA-Seq of formalin-fixed, paraffin-embedded (FFPE) and other low-quality samples offers valuable insights for disease research.
Paired-end RNA-Seq enables discovery applications such as detecting gene fusions and characterizing novel splice isoforms.
BRC-Seq uses BaseSpace for sample tracking as well as data analysis, management, and sharing.
Identify sequencing panels or microarrays that target your genes of interest.
*Data calculations on file. Illumina, Inc., 2015