NextSeq 550 System applications and methods

A wide world of inquiry

Harness next-generation sequencing and array technologies to do more with a single system

Key applications and methods

mRNA sequencing
Exome sequencing
Small whole-genome sequencing

The NextSeq 550 System RNA sequencing solution enables researchers to examine gene expression and identify isoforms, novel transcripts, and gene fusions. mRNA sequencing delivers a detailed snapshot of the coding transcriptome, enabling sequencing of up to 16 transcriptomes per run.

See how researchers use mRNA-Seq with the NextSeq 550 System:

Sifting through cells

Discovering cancer biomarkers

NextSeq 550 System RNA-Seq application note

Prep

Illumina Stranded mRNA Prep

A simple, scalable, cost-effective, rapid single-day solution for analyzing the coding transcriptome using as little as 25 ng input of standard (nondegraded) RNA.

Sequence

NextSeq 500/550 v2.5 Reagent Kits

Ready-to-use reagent kits include the reagent cartridge, flow cell, and buffer for use with the NextSeq 550 System. Multiple sequencing output and read length options available.

Analyze

DRAGEN RNA

Next-generation sequencing secondary analysis of RNA transcripts, including alignment, quantification, and fusion detection.

RNA-Seq Differential Expression

Differential expression analysis of reference genes with DESeq2.

Find mRNA-Seq education

The NextSeq 550 System offers a simple and reliable method to identify coding variants by accurately sequencing even the most difficult genomic regions. Exome sequencing analyzes the protein-coding region of the genome, as a cost-effective alternative to whole-genome sequencing. The NextSeq 550 System can sequence 3–12 exomes per run.

See how researchers use exome sequencing with the NextSeq 550 System:

HLA genetics and autoimmune disease

Cancer biomarker discovery

NextSeq 550 exome application note

Prep

Illumina DNA Prep with Enrichment

Fast, user-friendly workflow that combines on-bead tagmentation with a simplified, single- hybridization protocol to reduce total workflow time.

Sequence

NextSeq 500/550 v2.5 Reagent Kits

Ready-to-use reagent kits include the reagent cartridge, flow cell, and buffer for use with the NextSeq 550 System. Multiple sequencing output and read length options available.

Analyze

DRAGEN Enrichment

Aligns and calls variants from FASTQ, BAM, or CRAM files, outputting BAM and VCF files.

Find exome sequencing education

The NextSeq 550 System sequences up to 384 small genomes per run to provide a detailed view of the genomes of the smallest organisms. Small whole-genome sequencing (WGS) enables comprehensive analysis of microbial or viral genomes for applications in public health, infectious disease surveillance, molecular epidemiology studies, and environmental metagenomics.

Prep

Illumina DNA Prep

Fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species.

Nextera XT DNA Library Preparation Kit

Rapid library prep optimized for small genomes, PCR amplicons, and plasmids, requiring as little as 1 ng of input and 15 minutes of hands-on-time.

Sequence

NextSeq 500/550 v2.5 Reagent Kits

Ready-to-use reagent kits include the reagent cartridge, flow cell, and buffer for use with the NextSeq 550 System. Multiple sequencing output and read length options available.

Analyze

BaseSpace Sequence Hub Whole Genome Sequencing App

Quickly extracts biological information from whole-genome sequences using Isaac Alignment and variant calling.

Find small WGS education

More applications and methods

Amplicon sequencing

Perform ultra-deep sequencing of PCR amplicons with cost-effective analysis of up to hundreds of target genomic regions in one assay.

Learn more about amplicon sequencing

Read application note

Methylation sequencing

Enhance epigenetic studies with high-coverage density and flexibility enabled by sequencing-based DNA methylation analysis.

Learn more about methylation sequencing

Coding transcriptome analysis

Detect both known and novel features of the coding transcriptome using sequence-specific capture of RNA coding regions.

Learn more about coding transcriptome analysis

Microarray scanning

Scan Illumina microarrays with rapid, sensitive, and accurate imaging for exceptional genetic analysis.

Learn more about microarray scanning

Cytogenetic microarrays and sequencing

Perform sequencing and high-quality cytogenomic array-based analysis on a single platform for a range of constitutional and cancer research applications.

Learn more about cytogenetics

Read customer interview

miRNA and small RNA analysis

Isolate and sequence small RNA species, such as microRNA, to study the role of noncoding RNA in gene silencing and posttranscriptional regulation.

Learn more about small RNA analysis

Read customer interview

De novo sequencing

Enable fast, accurate characterization of novel genomes with no reference sequence available for any species.

Learn more about de novo sequencing

RNA drug response biomarker discovery

Discover and profile RNA-based drug response biomarkers to help improve the efficiency and success rate of drug development.

Learn more about RNA drug response biomarkers

ChIP-Seq

Analyze protein interactions with DNA for genome-wide surveys of gene regulation.

Learn more about ChIP-Seq

Read customer interview

Target enrichment

Use sequence-specific hybridization to analyze genomic regions of interest.

Learn more about target enrichment

Genotyping by sequencing

Discover novel plant and animal SNPs and perform genotyping studies with a low-cost genetic screening method.

Learn more about genotyping by sequencing

Targeted DNA sequencing

Focus time, expenses, and analysis on sequencing only a subset of genes or genome regions of research interest.

Learn more about targeted DNA sequencing

Read article

Metagenomics

Assess genes in organisms present in a complex sample to evaluate bacterial diversity and detect unculturable microorganisms.

Learn more about metagenomics

Read application note

Translation analysis

Monitor cellular translation processes and determine what regions of a message are being translated with ribosome profiling.

Learn more about translation analysis

Read application note

Read customer interview

Methylation arrays

Interrogate CpG sites at single-nucleotide resolution to get valuable insights into the regulation of gene expression.

Learn more about methylation arrays

Total RNA sequencing

Analyze coding RNA plus multiple forms of noncoding RNA for a comprehensive picture of the transcriptome.

Learn more about total RNA-Seq

Read application note

Read customer interview

How others use this instrument

See what’s possible with the flexible NextSeq 550 System

NGS identifies rare disease variants in infants with undiagnosed disease

Discover how the Singapore Undiagnosed Diseases Research program for Kids (SUREKids) uses WES on the NextSeq 550 System to identify new rare disease-associated variants.

eDNA sequencing offers a powerful lens to view changes in biodiversity

Learn how the NextSeq 550 System enables shotgun sequencing of coral and fish mitochondrial genomes for environmental and biodiversity research.

Illumina financial solutions

NextSeq 1000 and NextSeq 2000 Reagents

Sequencing Platform Comparison Tool

Rethink what’s possible with DRAGEN analysis

Illumina Proactive Instrument Performance Service

Do more, faster than ever

Learning about our own genomes through primates

Learning about our own genomes through primates

Learning about our own genomes through primates

Learning about our own genomes through primates

Learning about our own genomes through primates

Learning about our own genomes through primates

Learning about our own genomes through primates

This is the Genome Era

This is the Genome Era

This is the Genome Era

This is the Genome Era

This is the Genome Era

This is the Genome Era

This is the Genome Era

Illumina DRAGEN Secondary Analysis v4.2

Illumina DRAGEN Secondary Analysis v4.2

Illumina DRAGEN Secondary Analysis v4.2

Illumina DRAGEN Secondary Analysis v4.2

Illumina DRAGEN Secondary Analysis v4.2

Illumina DRAGEN Secondary Analysis v4.2

TruSight Oncology 500 ctDNA v2 is now available

TruSight Oncology 500 ctDNA v2 is now available

TruSight Oncology 500 ctDNA v2 is now available

TruSight Oncology 500 ctDNA v2 is now available

TruSight Oncology 500 ctDNA v2 is now available

“Tripledemic” pathogen surveillance is critical

“Tripledemic” pathogen surveillance is critical

“Tripledemic” pathogen surveillance is critical

“Tripledemic” pathogen surveillance is critical

“Tripledemic” pathogen surveillance is critical

The race results are in—with marine genomic data

The race results are in—with marine genomic data

The race results are in—with marine genomic data

The race results are in—with marine genomic data

The race results are in—with marine genomic data

Shriners Children’s and specialized pediatric care

Shriners Children’s and specialized pediatric care

Shriners Children’s and specialized pediatric care

Shriners Children’s and specialized pediatric care

Shriners Children’s and specialized pediatric care

“Tripledemic” pathogen surveillance is critical

“Tripledemic” pathogen surveillance is critical

“Tripledemic” pathogen surveillance is critical

“Tripledemic” pathogen surveillance is critical

“Tripledemic” pathogen surveillance is critical

A new era for clinical labs

A new era for clinical labs

A new era for clinical labs

A new era for clinical labs

A new era for clinical labs

A new era for clinical labs

A new era for clinical labs

A new era for clinical labs

Announcing Illumina Complete Long Reads

Announcing Illumina Complete Long Reads

Announcing Illumina Complete Long Reads

Announcing Illumina Complete Long Reads

NextSeq 550 System applications and methods

Key applications and methods

Prep

Sequence

Analyze

Prep

Sequence

Analyze

Prep

Sequence

Analyze

High-impact discovery through gene expression and regulation research

More applications and methods

Amplicon sequencing

Methylation sequencing

Coding transcriptome analysis

Microarray scanning