Create a global picture of cell function

Fully characterize gene expression and transcriptome changes for a deeper understanding of biology

Gene Expression and Transcriptome Analysis

Transcriptome analysis experiments can characterize all transcriptional activity (coding and non-coding), focus on a subset of relevant target genes and transcripts, or profile thousands of genes at once to create a global picture of cell function. Gene expression analysis studies can provide a snapshot of actively expressed genes and transcripts under various conditions.

Illumina offers comprehensive next-generation sequencing (NGS) and array solutions that provide high-quality gene expression and transcriptome analysis data for a broad range of sample types. NGS-based RNA sequencing (RNA-Seq) methods can quantify and profile any active gene or transcript, including novel transcripts. Expression microarray technology measures the relative activity of known, predefined genes and transcripts.

Introduction to  Transcriptome and Gene Expression Analysis

RNA-Seq provides a unique combination of transcriptome-wide coverage, sensitivity, and accuracy for a comprehensive view of gene expression changes. Illumina RNA-Seq solutions provide precise measurement of strand orientation, uniform coverage, and high confidence mapping of alternate transcripts and gene fusions. Discover novel gene isoforms, profile gene expression for select targets of interest, analyze the whole coding transcriptome, and accurately perform transcript abundance and fold-change measurement.

Learn more about:

  • mRNA Sequencing: Discover alternative transcripts, gene fusions, and allele-specific expression patterns with a clear, complete view of the coding transcriptome.
  • Targeted RNA Sequencing: Select and sequence specific genes or transcripts of interest. Profile expression of dozens to thousands of target genes or transcripts simultaneously.
Targeted RNA-Seq on the MiniSeq System

The small and robust MiniSeq Benchtop Sequencer supports cost-efficient gene expression profiling, even for low numbers of samples.

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Capture the broad effects of gene expression changes using whole-transcriptome analysis with total RNA sequencing (total RNA-Seq). The method detects both coding and multiple forms of noncoding RNA for a comprehensive view of the entire transcriptome. Learn more about total RNA-Seq.

Whole-Transcriptome Sequencer

Analyze up to 10 transcriptomes in a single run with the NextSeq Series desktop sequencing system.

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Sequencing Method Explorer

Use the beta version of this interactive tool to explore experimental next-generation sequencing (NGS) library preparation methods compiled from the scientific literature. New methods will be continuously added.

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Method Selector

Expression arrays detect known, predefined genes and transcripts. With a low per-sample cost and high-throughput processing capabilities, Illumina genome-wide expression arrays generate high-quality data for large-scale expression analysis studies. Learn more about gene expression arrays.

From Arrays to mRNA-Seq

Expression Analysis scientists discuss transitioning from microarrays to mRNA-Seq.

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Cancer Transcriptome Analysis
Cancer Transcriptome Analysis

Profiling gene expression and transcriptome changes with RNA sequencing can aid in understanding tumor classification and progression. Learn more about cancer RNA-Seq.

Microbial Transcriptome Analysis
Microbial Transcriptome Analysis

Bacterial, viral, and other microbial RNA-Seq experiments enable annotation and quantification of comprehensive microbial transcripts. Learn more about microbial RNA-Seq.

Complex Disease Research
Complex Disease Research

Find out how genomic technologies are introducing new avenues for understanding complex disease etiology on a molecular level. Learn more about complex disease genomics.

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Analyze Gene Expression in Single Cells
Analyze Gene Expression in Single Cells

Highly sensitive RNA-Seq methods enable gene expression analysis of very low-input samples, even single cells.

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RNA-Seq Data Analysis
RNA-Seq Data Analysis

User-friendly BaseSpace Apps simplify analysis of gene expression data from RNA-Seq studies.

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RNA-Seq with NextSeq 500
RNA-Seq with NextSeq 500

NextSeq provides the power and versatility needed to address the full range of transcriptome analysis needs.

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Illumina NGS Application Guide
Illumina NGS Methods Guide

All the information you need, from library preparation to sequencer selection to analysis. Select the best tools for your lab.

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TruSeq Targeted RNA Expression kits
Gene Expression Profiling and Validation

TruSeq Targeted RNA Expression Kits offer highly customizable mid- to high-plex gene expression profiling and validation.

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RNA-Seq for Gene Expression Analysis

Illumina offers a complete, accessible RNA-Seq workflow solution for gene expression and transcriptome profiling studies.

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