Create a global picture of cell function

Profile gene expression and transcriptome changes for a deeper understanding of biology

Gene Expression and Transcriptome Analysis

Transcriptome analysis experiments enable researchers to 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.

Next-generation sequencing (NGS) capabilities have shifted the scope of transcriptomics from the interrogation of a few genes at a time to the profiling of genome-wide gene expression levels in a single experiment. Find out how to analyze gene expression and identify novel transcripts using NGS-based RNA sequencing (RNA-Seq) methods. Illumina offers comprehensive solutions for a broad range of sample types.

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 methods 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 coding transcriptome, and accurately measure transcript abundance and fold changes in expression.

Learn how to analyze gene expression using the following NGS-based RNA-Seq methods:

  • mRNA Sequencing: Discover alternative transcripts, gene fusions, and allele-specific expression patterns with a clear, comprehensive view of the coding transcriptome.
  • Targeted RNA Sequencing: Select and sequence specific genes or transcripts of interest. Profile gene expression for dozens to thousands of targets simultaneously.
Advantages of Gene Expression Profiling with RNA-Seq

Explore the benefits of NGS for analysis of gene expression, gene regulation, and methylation. Learn how RNA-Seq methods are accelerating research in a broad range of fields, from cancer to cell biology, microbiology, drug discovery, and more.

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

AmpliSeq for Illumina Transcriptome Human Gene Expression Panel

Targeted research panel that measures expression levels of >20,000 human RefSeq genes.

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Uncovering Drug-Susceptible Tumorigenic Pathways

Researchers use Illumina sequencing to profile biomarkers and analyze transcriptome signatures of activated pathways in cancer samples.

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Cancer Driver Gene Expression Analysis

Researchers use whole-genome sequencing to predict cancer gene expression status based on nucleosome patterns, and RNA-Seq to confirm gene expression.

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Gene Panel and Array Finder

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

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Gene Panel and Array 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 solution for analyzing gene expression, allowing researchers to detect both known and novel genes and transcripts in a single assay.  Learn more about RNA-Seq advantages over arrays.

More Funding for Multi-Method Studies

Grant funding for studies using multiple genomic methods has increased since 2010.* Explore various resources to see how the use of multiple genomic methods is having an impact on research.

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Cancer Gene Expression Profiling
Cancer Transcriptome Analysis

Analyzing gene expression and transcriptome changes with RNA sequencing can help researchers understand 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

Gene expression and transcriptome profiling studies can help researchers better understand neurological, immunological, and other complex diseases on a molecular level. Learn more about complex disease genomics.

Drug Response Biomarker Studies
RNA-Based Drug Response Biomarker Analysis

Find out how to utilize RNA-Seq to discover and profile RNA-based drug response biomarkers. Access resources designed to help researchers adopt this application. Learn more about drug response RNA biomarker analysis.

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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 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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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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Untangling Alzheimer's Secrets
Untangling Alzheimer's Secrets

Amanda Myers, PhD uses a combination of genomics, transcriptomics, and proteomics to explain the complexity of Alzheimer’s disease.

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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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References

*Based on National Institutes of Health (NIH) funding. Data calculations on file. Illumina, Inc., 2017.