Key methods on the HiSeq 2500 System

Exome, targeted resequencing, whole-transcriptome and de novo sequencing, epigenetic regulation, and more

HiSeq 2500 Applications and Methods

Exome sequencing analyzes the protein-coding region of the genome, as a cost-effective alternative to whole-genome sequencing. With both rapid Run and High Output modes, HiSeq 2500 System is a flexible system that can sequence 5–75 exomes* per run.

*Assumes 100x coverage with 80% on target using 2 x 75 bp reads.

Analyze both coding RNA and multiple forms of noncoding RNA with total RNA sequencing (RNA-Seq) for a comprehensive view of the transcriptome. With 4 billion reads per dual flow cell HiSeq run using the HiSeq v4 chemistry, the HiSeq 2500 System can sequence up to 80 transcriptomes* per run.

*Assumes 50 million reads per sample.

See how researchers are using total RNA-Seq on the HiSeq Series.

Gene Expression Profiling

mRNA sequencing (mRNA-Seq) detects known and novel transcripts and measures transcript abundance for accurate, comprehensive expression profiling.

Learn More
Large Whole-Genome Sequencing

Sequencing large complex genomes (human, plant, or animal) provides a base-by-base view of genomic alterations to inform studies of disease or population genomics.

Researcher Interview

Bringing Sunflower Breeding into the Genomics Era

Learn More
DNA-Protein Interaction Analysis

Combining chromatin immunoprecipitation (ChIP) assays with sequencing, ChIP-Seq is a powerful method for genome-wide surveys of gene regulation.

Learn More
Methylation Sequencing

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

Researcher Interview

Mysteries of Metastasis

Learn More
Coding Transcriptome Analysis

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

Learn More
De Novo Sequencing

With a unique mix of high output, long reads, and paired-end sequencing, HiSeq is a powerful tool for de novo sequencing of species without a reference genome.

Researcher Interview

Assembling the Kiwi Genome

Learn More
Metagenomics

Perform metagenomic analyses by sequencing entire microbial communities to discover important taxonomic and functional information.

Researcher Interview

Studying Microorganisms along the Mississippi River

Learn More
Genotyping by Sequencing

Genotyping by sequencing provides a low-cost genetic screening method to discover novel plant and animal SNPs and perform genotyping studies.

Researcher Interview

Restoring and Managing Fish Populations with Genomics

Learn More
Small Whole-Genome Sequencing

Small genome sequencing provides comprehensive analysis of microbial or viral genomes for public health, epidemiology, and disease studies.

Learn More
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
Targeted Gene Panels

Targeted gene sequencing panels contain defined probe sets focused on specific genes of interest. Both predesigned and custom panels are available.

Learn More
16S rRNA Sequencing

A culture-free method to identify and compare bacteria from complex microbiomes or environments that are difficult to study.

Learn More
Translation Analysis

Ribosome profiling enables systematic monitoring of cellular translation processes and prediction of protein abundance.

Learn More
Targeted RNA Expression Analysis

Targeted RNA sequencing (RNA-Seq) focuses on specific transcripts of interest, used to analyze gene expression and identify fusion genes.

Learn More
Amplicon Sequencing

Ultra-deep sequencing of PCR amplicons enables cost-effective analysis of up to hundreds of target genomic regions in one assay.

Learn More
Cytogenomics

Next-generation sequencing offers base-by-base, genome-wide detection of chromosomal variation to complement array-based cytogenomic analysis.

Learn More
Population Studies

Robust, secure, and scalable platforms to aggregate and interpret large-scale genomic data for population sequencing applications.

Researcher Interview

Witnesses to a Sea Change in Sequencing Capability

Learn More
Sample Quality Control

Assess the quality of a sequencing library before committing it to a full-scale run, or perform quality control applications for bioproduction studies.

Learn More
Illumina NGS Methods Guide

Illumina NGS Methods Guide

Access the information you need—from genome, transcriptome, or epigenome library preparation 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