Key methods on the HiSeq 3000/HiSeq 4000 Systems

Speed, flexibility, and performance for production-scale sequencing across multiple applications, species, and sample types

HiSeq 3000/HiSeq 4000 Applications and Methods

Exome sequencing analyzes the protein-coding region of the genome, as a cost-effective alternative to whole-genome sequencing. The HiSeq 4000 System can sequence up to 96 exomes* per run.

Application Note: Genome, Exome, and Transcriptome Analysis on the HiSeq 4000 System

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

Whole-genome sequencing (WGS) analysis of large complex genomes (human, plant, or animal) provides a base-by-base view of genomic alterations to inform studies of disease or population genomics. The HiSeq 4000 System can sequence up to 12 human genomes* per run.

Application Note: Genome, Exome, and Transcriptome Analysis on the HiSeq 4000 System

*Assumes >30× coverage of a human genome.

Analyze both coding RNA and multiple forms of noncoding RNA with total RNA sequencing (RNA-Seq) for a comprehensive view of the transcriptome. The HiSeq 4000 System can sequence up to 100 transcriptomes* per run.

Application Note: Genome, Exome, and Transcriptome Analysis on the HiSeq 4000 System

*Assumes 50 million reads per sample.

Methylation Sequencing

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

Application Note:

Whole-Genome Bisulfite Sequencing on the HiSeq 3000/HiSeq 4000 Systems

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Gene Expression Profiling

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

Application Note:

Genome, Exome and Transcriptome Analysis on the HiSeq 4000 System

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Coding Transcriptome Analysis

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

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DNA-Protein Interaction Analysis

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

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Targeted DNA Sequencing

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

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Small Whole-Genome Sequencing

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

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De Novo Sequencing

De Novo sequencing refers to sequencing a novel genome with no reference sequence available. NGS enables fast, accurate characterization of any species.

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16S rRNA Sequencing

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

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Translation Analysis

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

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miRNA & Small RNA Analysis

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

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Metagenomics

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

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Genotyping by Sequencing

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

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Cytogenomics

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

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Targeted RNA Expression Analysis

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

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Targeted Gene Panels

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

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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.

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