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 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) 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.

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.
Empowering Transcriptomics with RNA Sequencing

This ebook discusses genomics applications in gene expression and regulation research. See how workflows can impact study results.

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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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Gene Panel Finder

Next-generation sequencing (NGS) offers the scalability, speed, and resolution for targeted resequencing. Our Gene Panel Finder will help you identify predesigned Illumina sequencing panels to match your genes of interest.

Find the Right Panel
Gene Panel Finder

While gene expression microarrays are effective for identifying the expression of known genes and transcripts, they cannot detect previously unidentified transcripts. In contrast, RNA-Seq offers a comprehensive gene expression profiling solution, allowing researchers to detect both known and novel genes and transcripts in a single assay.  Learn more about RNA-Seq advantages over arrays.

From Arrays to mRNA-Seq

Expression Analysis scientists discuss transitioning from microarrays to mRNA-Seq, and describe their comparison studies.

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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 software tools simplify mRNA-Seq data analysis for biologists, regardless of bioinformatics experience.

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RNA-Seq with the NextSeq Series
RNA-Seq with the NextSeq Series

A flexible, cost-effective solution for RNA sequencing provides a deeper understanding of biology.

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Methods Guide
Methods Guide

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

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Gene Expression Profiling and Validation
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
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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Sequencing Method Explorer
Sequencing Method Explorer

Use this interactive tool to explore experimental NGS library preparation methods compiled from the scientific literature.

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Single-Cell RNA Sequencing
Single-Cell RNA Sequencing

Providing a high-resolution view of cell-to-cell variation.

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