Key Applications and Methods
mRNA sequencing (mRNA-Seq) enables researchers to take a closer look at gene expression and can be used to identify isoforms, novel transcripts, and gene fusions. The NextSeq 550 RNA sequencing solution leverages proven Illumina technology to deliver a detailed snapshot of the coding transcriptome. Sequence up to 16 transcriptomes per NextSeq 550 run.
See how researchers use mRNA-Seq with the NextSeq 550 System.
Read eBook: Gene Expression and Regulation Research with RNA-Seq
Library Prep
10.5 hours/4.5 hours hands-on
TruSeq Stranded mRNA Library Prep Kit
Prepare sequencing libraries from mRNA to get a clear view of the coding transcriptome with strand-specific information.
Sequence
15–18 hours/15 minutes hands-on
NextSeq 500/550 v2.5 Reagent Kits
Bring the power of a high-throughput sequencing system to the benchtop. The 150 cycle high-output or mid-output kits provide 2 x 75 bp reads for total RNA-Seq.
Analyze
Push-button tools
DRAGEN RNA Pipeline
Performs alignment, quantification, and fusion detection.
RNA-Seq Differential Expression
Enables differential gene expression analysis.
Exome sequencing analyzes the protein-coding region of the genome, as a cost-effective alternative to whole-genome sequencing. Exome sequencing with the NextSeq 550 System offers a simple and reliable method to identify coding variants, successfully sequencing even the most difficult genomic regions. Sequence 3–12 exomes per NextSeq run.
See how researchers use the NextSeq 550 System for exome sequencing applications.
Library Prep
1 day/3 hours hands-on
Nextera DNA Exome
Uses a simple, one-day workflow to provide a fast path to greater understanding of the human exome.
Nextera Flex for Enrichment
Nextera Flex for Enrichment uses a fast, user-friendly workflow. On-bead tagmentation chemistry is combined with a simplified, single hybridization protocol to reduce total workflow time.
Sequence
15-18 hours/15 minutes hands-on
NextSeq 500/550 v2.5 Reagent Kits
Bring the power of a high-throughput sequencing system to the benchtop. The 150 cycle high-output or mid-output kits provide 2 x 75 bp reads for total RNA-Seq..
Analyze
Push-button tools
DRAGEN Germline or Somatic Pipelines on the DRAGEN Server or the DRAGEN Enrichment App on BSSH
The on-premises DRAGEN Sever and DRAGEN on BaseSpace Sequence Hub offer rapid, accurate analysis of germline and somatic exome data.
The NextSeq 550 System leverages proven Illumina sequencing technology, delivering high coverage to identify variants throughout the genome. With push-button sequencing and minimal hands-on time, the NextSeq whole-genome sequencing (WGS) solution enables researchers to analyze any genome efficiently, from microbes to humans. Sequence 1 human genome or up to 384 small genomes per NextSeq run.
See how researchers can use the NextSeq 550 System to sequence whole genomes:
Library Prep
6 hours/4 hours hands-on
TruSeq Nano DNA Library Prep Kit
Generate WGS libraries and efficiently interrogate samples with limited available DNA.
Nextera DNA Flex Library Prep Kit
A fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species.
Sequence
26–29 hours/15 minutes hands-on
NextSeq 500/550 v2.5 Reagent Kits
Bring the power of a high-throughput sequencing system to the desktop. The 300 cycle high-output kit provides 2 x 150 bp reads for whole-genome sequencing.
Analyze
Push-button tools
BaseSpace Whole-Genome Sequencing App
Quickly extracts biological information from whole-genome sequences, using Isaac alignment and variant calling.
DRAGEN Germline Pipeline (on BSSH or on DRAGEN server)
The DRAGEN Germline Pipeline v3 aligns and optionally variant calls FASTQ files, outputting a BAM, VCF, or both.
DRAGEN Somatic Pipeline (on BSSH or on DRAGEN server)
The DRAGEN Somatic Pipeline aligns and variant calls Tumor-only or Tumor/Normal FASTQ files, outputting BAM(s) and a VCF.
Browse sample data sets on Basespace Sequence Hub:
NextSeq 550 v.2.5 WGS Run
NextSeq 550 v2.5 WGS Project
Featured Stories
Seeking the Source of Bacterial Drug Resistance
A targeted deep sequencing assay identifies multi-drug-resistant tuberculosis strains responsible for silent outbreaks.
Read Article
NGS Identifies Rare Disease Variants in Infants with Undiagnosed Disease
Landmark NGS study leads to a national clinical diagnostic exome sequencing platform in Singapore.
Read Interview
Uncovering the Intracellular Communication of Tumors
The microenvironment surrounding tumors could tell us more about how cancer cells migrate and become drug resitant.
Read InterviewSingle-Cell Analysis is Fueling New Discoveries in Developmental Biology
A computer scientist is expanding the reach of scRNA-Seq data through new open source technologies.
Read Interview
More Applications and Methods
Microarray Scanning
In addition to sequencing, the NextSeq 550 enables microarray scanning for a broad range of applications in reproductive health, genetic health, and cancer research, including methylation analysis with the Infinium MethylationEPIC BeadChip.
Target Enrichment
Use sequence-specific hybridization to analyze genomic regions of interest.
Whole-Transcriptome Sequencing
Analyze both coding RNA and multiple forms of noncoding RNA with total RNA sequencing, for a comprehensive view of the transcriptome.
Application Note
NextSeq 550 System RNA-Seq Solution
Researcher Interview
Coding Transcriptome Analysis
Detect both known and novel features of the RNA exome using sequence-specific capture of RNA coding regions.
Targeted DNA Resequencing
Targeted resequencing focuses time, expenses, and analysis on sequencing only a subset of genes or genome regions of research interest.
Researcher Interview
Targeted Gene Panels
Targeted gene sequencing panels contain defined probe sets focused on specific genes of interest. Both predesigned and custom panels are available.
Methylation Sequencing
Perform epigenetic studies with high-coverage density and flexibility enabled by sequencing-based DNA methylation analysis.
Amplicon Sequencing
Ultra-deep sequencing of PCR amplicons enables cost-effective analysis of up to hundreds of target genomic regions in one assay.
Application Note
De Novo Sequencing
De novo sequencing with next-generation sequencing (NGS) enables fast, accurate characterization of species without a reference genome.
Application Note
NextSeq 550 System WGS Solution
Researcher Interview
Delivering Sequencing Results Quickly and at a Competitive Price
Genotyping by Sequencing
Genotyping by sequencing provides a low-cost genetic screening method to discover novel plant and animal SNPs and perform genotyping studies.
DNA-Protein Interaction Analysis with ChIP-Seq
Combining chromatin immunoprecipitation (ChIP) assays with sequencing, ChIP-Seq is a powerful method for genome-wide surveys of gene regulation.
Researcher Interview
miRNA & 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.
Researcher Interview
Translation Analysis
Ribosome profiling enables systematic monitoring of cellular translation processes and prediction of protein abundance.
Application Note
Ribosome Profiling Enables Comprehensive Translation Analysis
Researcher Interview
Metagenomics
Comprehensively sample genes in organisms present in a complex sample to evaluate bacterial diversity and detect unculturable microorganisms.
Application Note
Cytogenomic Microarrays and Sequencing
Next-generation sequencing offers base-by-base, genome-wide detection of chromosomal variation to complement array-based cytogenomic analysis.
Researcher Interview
RNA Drug Response Biomarker Discovery
Find out how to utilize RNA-Seq to discover and profile RNA-based drug response biomarkers. Access resources designed to help new users adopt this application.
Methylation Arrays
Quantitatively interrogate methylation sites across the genome at single-nucleotide resolution.
Environmental DNA Sequencing
Environmental DNA (eDNA) sequencing is a rapidly emerging method for studying biodiversity and monitoring ecosystem changes.
Researcher Interview
eDNA Sequencing Offers a Powerful Lens to View Changes in Biodiversity
Methods Guide
Access the information you need—from BeadChips to library preparation for genome, transcriptome, or epigenome studies to sequencer selection, analysis, and support—all in one place. Select the best tools for your lab with our comprehensive guide designed specifically for research applications.
Access Guide