The most complete picture of the transcriptome

Capture the broadest possible range of transcripts from both coding and noncoding RNA species

Total RNA Sequencing

Whole-transcriptome analysis with total RNA sequencing (RNA-Seq) detects coding plus multiple forms of noncoding RNA. Total RNA-Seq can accurately measure gene and transcript abundance, and identify known and novel features of the transcriptome.

Total RNA-Seq provides optimal coverage in normal or low-quality samples. Species-specific ribosomal RNA probes (Ribo-Zero chemistry) can efficiently remove abundant RNA species. This leaves both fragmented and intact transcripts of interest for library capture.

Total RNA-Seq analyzes both coding and multiple forms of noncoding RNA for a comprehensive view of the transcriptome.

  • Captures both known and novel features
  • Allows researchers to identify biomarkers across the broadest range of transcripts
  • Enables a more comprehensive understanding of phenotypes of interest
  • Allows profiling of the transcriptome across a wide dynamic range
Advantages of Total RNA Sequencing

Dr. Avrum Spira, a pulmonary and critical care physician at Boston University Medical Center, started a lab with the goal of analyzing clinical samples with whole-genome gene expression arrays, to study potential biomarkers for future diagnosis and treatment of pulmonary disorders. Learn how Spira’s lab uses total RNA-Seq to uncover novel and rare transcripts that may not be detectable on expression arrays.
Read Case Study.

Transitioning from Whole-Genome Arrays to Total RNA Sequencing

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 total RNA-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 Total RNA with Ribo-Zero Kits:
Provide a complete view of the whole transcriptome with precise strand orientation measurement. FFPE RNA-compatible.
Compare Total RNA-Seq Library Prep Kits

Determine the best kit for your needs.

NextSeq Series

Flexible power and simplicity for whole genome, exome, or transcriptome sequencing. 3-10 total RNA samples per run.

HiSeq 2500 System

Power and efficiency to sequence 8-96 total RNA samples per run.

HiSeq 3000/HiSeq 4000 Systems

High-throughput RNA-Seq, with up to 50 human transcriptomes per run on the HiSeq 3000 and 100 transcriptomes on the HiSeq 4000.

NovaSeq Series

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 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.

The Broad’s IGV

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

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.

Cancer Research: Variant Detection
Cancer Research: Variant Detection

Monitoring gene expression changes in both coding and noncoding RNA biomarkers with total RNA-Seq can help researchers understand which variants affect tumor classification and progression. Learn more about cancer RNA-Seq.

Agrigenomics: Deep Transcriptome Sequencing
Agrigenomics: Deep Transcriptome Sequencing

Plants have large, repetitive genomes, which can make it difficult to sequence weakly expressed genes. Ultradeep RNA sequencing can facilitate analysis of these genes. Learn more about plant sequencing for agrigenomics.

Complex Disease: Biomarker Identification with RNA-Seq
Complex Disease: Biomarker Identification with RNA-Seq

Total RNA-Seq allows complex disease researchers to study coding and multiple forms of noncoding RNA in a single analysis, providing visibility to a broader range of potential disease-associated biomarkers. Learn more about complex disease research.

Recent Publications
High-throughput screening using patient-derived tumor xenografts to predict clinical trial drug response.

Nat Med 6 2015

View Summary
Transient acquisition of pluripotency during somatic cell transdifferentiation with iPSC reprogramming factors.

Nat Biotechnol 33 769-742015

View Summary
Global Promotion of Alternative Internal Exon Usage by mRNA 3' End Formation Factors.

Mol Cell 58 819-312015

View Summary
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RNA-Seq Data Analysis
RNA-Seq Data Analysis

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

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Total 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.

Learn More
Webinar: FFPE RNA-Seq
Webinar: FFPE RNA-Seq

Learn how to overcome hurdles in FFPE RNA sequencing.

Download Webinar
RNA-Seq on the NextSeq 500 System
RNA-Seq on the NextSeq Series

This solution for whole-transcriptome analysis with total RNA-Seq provides a deeper understanding of biology.

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Key RNA-Seq Publications
Key RNA-Seq Publications

View a searchable list of RNA-Seq research publications featuring Illumina technology.

View Publications
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.

Learn More
RNA-Seq and Single-Cell Sequencing
Introduction to Single-Cell Sequencing

Single-cell sequencing studies are on the rise with applications in a myriad of fields.

View Video

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