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.
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.
Illumina sequencing by synthesis (SBS) chemistry is the most widely adopted 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.
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 Series
Scalable throughput and flexibility for virtually any genome, sequencing method, and scale of project.
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.
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.
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.
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.
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.
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.
*Data calculations on file. Illumina, Inc., 2015