Illumina HiSeq 4000 Sequencing System


The Illumina HiSeq 4000 System Sequencer is a high-throughput DNA sequencer machine developed and manufactured by Illumina, and is designed for high throughput, production-scale sequencing laboratories. Built off the HiSeq 2500 System and harnessing the patterned flow cell technology originally developed for the HiSeq X™ Ten System, the Illumina HiSeq 4000 platform provides advanced speed and performance offering project design a significant capacity gain for a wide variety of sequencing investigations. Services used for this sequencing platform were contracted through GeneWiz (NGS platform resources).

HiSeq 4000 pre-processed raw data is packaged in a .fastq format and can be accessed at project dataset download DOI containing additional processed data products, metadata, and software related to a sequence analysis using deoxyribonucleic acid DNA sequencing products.

Data Source Contributions

Instrument Data Source Profile

Instrument Platform:       Illumina HiSeq 4000 System

Source Taxonomy:           Instrument > High Throughput Sequencer > Illumina HiSeq 4000 System Sequencer [EFO:0008563]

Data Type:                         Genomic dataset

Data Format:                     FASTQ format and Illumina native fastq format

Method Type:                    Nucleic acid identification and quantitation method > dual flow cell sequencing technology

Laboratory Technique:     Nucleic acid sequencing procedure > whole genome sequencing, exome sequencing, RNA-seq

Experimental Design:       Assay > Experimental Protocol > nucleic acid sequencing protocol

Research Topic Areas:     Scientific DataGenomicsSequencing > differential gene expression



This work was supported in part by the Earth and Biological Sciences Directorate (EBSD) at Pacific Northwest National Laboratory (PNNL), a multiprogram national laboratory managed by the Battelle Memorial Institute, operating under the U.S. Department of Energy (DOE) contract DE-AC05-76RL01830. User capabilities described here reflect collaborations with the Environmental Molecular Sciences Laboratory (EMSL), a DOE Office of Science (SC-3) user facility operating under the Contract No. DE-AC05-76RL01830.


Technical Note

The HiSeq 3000/HiSeq 4000 Systems has been discontinued. Illumina will provide full support of the instruments and supplied reagents through March 31, 2024. To find an alternative instrument, Illumina recommends using the Sequencing Platform Comparison Tool. For support contact,

Projects (1)

Last updated on 2023-02-23T19:37:46+00:00 by LN Anderson PerCon SFA Project Publication Experimental Data Catalog The Persistence Control of Engineered Functions in Complex Soil Microbiomes Project (PerCon SFA) at Pacific Northwest National Laboratory ( PNNL ) is a Genomic Sciences Program...

  1. Datasets

Datasets (1)
People (2)

Lindsey Anderson’s research has been dedicated to the identification and characterization of novel, targeted and non-targeted, functional metabolic interactions using a high-throughput systems biology and computational biology approach. Her expertise in functional metabolism and multidisciplinary...

Publications: 2018 Stegen JC, TC Johnson, JK Fredrickson, MJ Wilkins, AE Konopka, WC Nelson, EV Arntzen, WB Chrisler, RK Chu, SJ Fansler, EB Graham, DW Kennedy, CT Resch, MM Tfaily, and JM Zachara. 2018. "Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial...