Illumina technologies


Features of the HiSeq platforms

HiSeq 2000

The HiSeq 2000, installed in July 2011, is the flagship of the Illumina fleet of next-generation sequencers.  The instrument is capable of producing more than 40-60Gbp per run.  Each flow cell lane produces about 200-300 million clusters.

The HiSeq 2000 utilizes Illumina’s proven and widely-adopted, reversible terminator-based sequencing by synthesis chemistry.

The ultra-high output of the HiSeq 2000 now makes it possible to sequence more than six human genomes at ~30× coverage simultaneously.

Please visit the Illumina website for more information about HiSeq 2000 System Performance Parameters.

HiSeq 2500

The HiSeq 2500 system switches between High Output and Rapid Run modes giving you the flexibility to run any application, for a wide range of study sizes to suit your research needs. HiSeq 2500 can generate up to 600 Gb of data in a high output run, or 120 Gb in rapid run mode with paired 100bp runs. Hiseq 2500 systems are the first high output sequencing systems to support fully integrated work flows where everything including cluster generation, SBS sequencing, data analysis and data storage to the BaseSpace Cloud can be completed on a single instrument.

Please visit the Illumina website for more information about HiSeq 2500 System Performance Parameters.

Illumina MiSeq

The MiSeq personal sequencing system enables researchers to go from sample to analyzed data in as little as eight hours. MiSeq integrates amplification, sequencing, and data analysis in a single instrument. The MiSeq system leverages Illumina’s proven TruSeq® sequencing by synthesis chemistry, making it the ideal platform for anyone performing rapid and cost-effective genetic analysis for a wide range of applications. These include: targeted resequencing (amplicon sequencing, targeted enrichment, 16S metagenomics); small genome sequencing (both de novo and resequencing); RNA sequencing (small RNA and microbial RNA-Seq); library QC; and ChIP-seq.

MiSeq offers paired-end sequence reads of up to 250 bp, for a total of ~8G bases (approximately 15M high quality paired-end reads) in less than 48 hours.

Please visit the Illumina website for more information about MiSeq System Performance Parameters.

The BRF HiSeq service

Library construction

Library types available
DNA library
mRNA library
small RNA library
Mate pair library

ChIP libraries




Genotyping by Sequencing (GBS)

Other customised libraries (please contact the facility)



1.  DNA Sequencing

Illumina Hiseq produces sequence reads up to 150 bp, in either single read or paired-end read format. TruSeq sequencing chemistry supports a wide range of applications including whole-genome sequencing, targeted resequencing, de novo sequencing, SNP discovery, identification of copy number variations, and chromosomal rearrangement.

2. Gene Regulation Analysis

Illumina RNA sequencing enables deep profiling of the transcriptome. With RNA sequencing, you can characterize all transcriptional activity, coding and non-coding, in any organism, which allows you to annotate coding SNPs, discover transcript isoforms, identify regulatory RNAs, characterize splice junctions and determine the relative abundance of transcripts.  The TruSeq RNA sample prep kit provides 12  unique indexes which allows economical RNA sequencing for discovery and profiling.

3. SNP Discovery and Structural Variation Analysis

Single nucleotide polymorphisms (SNPs) and structural variants are at the root of genetic variation among individuals and populations.  This variation influences how individuals differ in their risk of disease and their response to therapeutic treatments.  SNPs and structural variants are discovered within the genome by comparing multiple genomic sequences from a diverse sample set of individuals. The Illumina platform provides high-quality data for accurate SNP discovery and structural variation analysis studies.

4. Cytogenetic Analysis

Structural variability is a substantial source of genetic variation that has a major influence on phenotypic variation. Cytogenetic analysis allows researchers to profile chromosomal aberrations such as amplifications, deletions, rearrangements, point mutations, copy number changes, and copy-neutral loss of heterozygosity (LOH) events.

5.  DNA-Protein Interaction Analysis (ChIP-Seq)

Accurately survey interactions between protein, DNA, and RNA to interpret regulation events central to many biological processes and disease states. Quantify in-vivo protein-DNA interactions using the combination of chromatin immunoprecipitation with Illumina's sequencing technology (ChIP-Seq) on a genome-wide scale. Identify a broad range of interactions with confidence, and use millions of counts to differentiate real events from noise.

6. Sequencing-based Methylation Analysis

Researchers identify and track methylation patterns by directly sequencing bisulfite-converted DNA, methylation-sensitive restriction digest-enriched fragments, anti-methyl C-precipitated fragments, or chromatin immunoprecipitates of methyltransferases trapped to aza-labeled DNA. Using Illumina sequencing technology, you can evenly sequence a repetitive bisulfite-converted genome and detect variations in methylation signatures at single-base resolution to pinpoint rare binding events to within 50 bases of the actual binding site.

7.  Small RNA Discovery and Analysis

SmallRNA assays enable the discovery and profiling of microRNAs and other non-coding RNA on any organism. Using low RNA inputs, you can profile the differential expression of known microRNAs as well as detect novel microRNA targets and wide-ranging sequence variation or "iso-miRs" miRBase accessions. Truseq small RNA library kit enables high-throughput miRNA profiling using up to 48 unique indexes for multiplexed sequencing.  High sensitivity assay can detect as low as a single copy per cell.

Acknowledgment:  the above information is drawn from Illumina


Please contact the BRF to enquire about price.

Phone: (612) 54326

Order form

Order forms for the following HiSeq services can be downloaded.

  1. BRF prepares library on behalf of customer
  2. Customer prepares library.

HiSeq 2000 order forms

BRF-made library (DOCX, 160KB)

Customer-made library (DOCX, 170KB)

HiSeq 2500 order forms

BRF-made library (DOCX, 160KB)

Customer-made library (PDF, 170KB)

MiSeq order forms

BRF-made library (PDF, 160KB)

Customer-made library (PDF, 171KB)

NextSeq 500 order forms

BRF-made library (DOCX, 160KB)

Customer-made library (DOCX, 173KB)


Terms & conditions


1. The BRF operates on a cost recovery basis.  The percentage of subsidization is determined by The John Curtin School of Medical Research.

2. No samples or orders will be processed without an authorised* sample submission/order form and valid charge code.

 (*Authorised by signature of the PI/Lab Head, or by granting of electronic access to BRF ordering systems with the authority of the PI/Lab Head).

3. It is a condition of the contract between the ACRF and JCSMR/ANU that "the Foundation (ACRF) is to be acknowledged in all scientific publications which utilise the Facility (BRF) at the Institute (JCSMR)". 
All work performed in the BRF, whether full service or not, and the use of any BRF resources should be acknowledged in all publications arising from that work. This should be in the “Material and Methods” section of the paper (see examples below). Any further individual acknowledgements are solely at your discretion.


A reference to the publication should be sent to the Manager of the BRF once the paper is published (includes theses).


BRF collaborations and co-authorship: although the BRF is primarily a service unit, there are instances where BRF staff make significant contributions to either the technical or intellectual input of the project. This should be discussed with the staff member concerned prior to commencement of the collaboration. 

Consumables and data

  1. The customer agrees to cover the cost of any consumables ordered on their behalf if the customer fails to supply the correct quantity and quality of the starting material required for processing. Details of the quality and quantity required are on the BRF website and sample submission form. 

  2. Customers are responsible for archiving data generated by the BRF. Data generated by the BRF are solely for the use of the customer and their collaborators. Data is not to be sold to a third party. 

 The BRF shall not be responsible for data output generated from samples that deviate from recommended protocols as requested by the customer.

  3. Upon receipt of consumables and/or data, the customer accepts responsibility for the correct handling, use, storage and disposal of the consumables/data.
  4. The BRF extends no warranties of any kind in respect to the consumables.

  Any consumables sold may have hazardous properties.  The customer agrees to use appropriate caution and safeguards as not all properties are known. 

  5. Consumables sold by the BRF shall not be transferred to another party without the written consent of the BRF.  The BRF is not responsible for any losses arising from the use of consumables. 

 The BRF will not be liable to the customer for any loss, claim or demand made by the customer due to acceptance, handling, use, storage or disposal of consumables and/or data by the customer, except to the extent permitted by law when it is the result of wilful misconduct on the part of the BRF or its employees.

Acknowledgement in Publications


Real-time PCR

“Amplifications were performed in 384-well optical reaction plates (Applied Biosystems) with a 7900HT Fast Real-Time PCR System at the Genome Discovery Unit - ACRF Biomolecular Resource Facility, The John Curtin School of Medical Research, Australian National University using SDS 2.4 software to analyse raw data.”

DNA Sanger Sequencing

“Amplified PCR products were purified and sequenced on an AB 3730xl DNA Analyzer (at the Genome Discovery Unit - ACRF Biomolecular Resource Facility, The John Curtin School of Medical Research, Australian National University) following the manufacturer's protocol (Applied Biosystems 2002).”

Peptide synthesis

“Peptides were synthesized chemically using the 9-fluorenylmethyloxycarbonyl (Fmoc) method on a CEM Microwave-assisted Peptide Synthesizer and purified by one round of C18 reversed-phase HPLC by the Genome Discovery Unit - ACRF Biomolecular Resource Facility at the John Curtin School of Medical Research, Australian National University. As required, the N- or C-terminus, or both, were protected by acetylation or amidation, respectively.” 

Tetramer synthesis

“Cells were surface stained with APC-labelled tetramers consisting of murine class I MHC molecule (H-2Db), b2-microglobulin and influenza nucleoprotein peptide NP366–374. Tetramers were synthesised at the Genome Discovery Unit - ACRF Biomolecular Resource Facility at The John Curtin School of Medical Research, Australian National University using BirA enzyme synthesized as described (O’Callaghan et al., 1999). [O’Callaghan, C.A., Byford, M.F., Wyer, J.R., Willcox, B.E., Jakobsen, B.K., McMichael, A.J. and Bell, J.I (1999). BirA Enzyme: Production and Application in the study of membrane receptor-ligand interactions by site-specific biotinylation.Anal. Biochem. 266, 9-15.]”

Updated:  21 August 2018/Responsible Officer:  Director, ACRF/Page Contact:  Web Admin, ACRF