A comprehensive picture of the transcriptome

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

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 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 whole 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 samples with whole-genome gene expression arrays, to study potential biomarkers for 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
Deciphering the Role of Long Non-Coding RNA in Cancer

Researchers are using total RNA-Seq to reveal how lncRNAs could be used to identify, measure, and treat cancer. Learn why total RNA-Seq offers advantages over polyA RNA-Seq.

Read Interview
Deciphering the Role of Long Non-Coding RNA in Cancer

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

In addition to high-quality data, Illumina offers integrated whole-transcriptome sequencing 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

Get a comprehensive view of the whole transcriptome with precise strand orientation measurement. FFPE RNA-compatible. Options include:

Find the Right Library Prep Kit

Determine the best kit for your needs.

NextSeq 550 System

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

HiSeq 4000 System

High-throughput RNA-Seq, with up to 100 human transcriptomes per run.

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 buffers tailored to each Illumina sequencing system.

BaseSpace RNA Express App

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

BaseSpace TopHat Alignment App

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

BaseSpace 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.

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.

RNA Sequencing Considerations

Each RNA-Seq experiment type—whether it’s gene expression profiling, targeted RNA expression, or small RNA analysis—has unique requirements for read length and depth. This bulletin reviews experimental considerations and offers resources to help with study design.

Read Bulletin
RNA Sequencing Considerations
Cancer Research: Gene Expression Studies
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
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 broad range of potential disease-associated biomarkers. Learn more about complex disease research.

RNA-Based Drug Response Biomarker Discovery
RNA-Based Drug Response Biomarker Analysis

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 RNA biomarker analysis for drug development.

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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.

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Webinar: FFPE RNA-Seq
Webinar: FFPE RNA-Seq

Learn how to overcome hurdles in FFPE RNA sequencing.

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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.

Access PDF
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.

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