We value the feedback from our customers. If you have any comments about our services you think may be useful for other researchers, please let us know by emailing us at sequencing@geneworks.com.au.


Here are some examples of customer experiences with GeneWorks services:

• Small RNA sequencing for discovery – Professor John Mattick, University of Queensland, Brisbane

• DeepCAGE analysis of transcription – Dr Clare Stirzaker, Garvan Institute of Medical Research, Sydney

• Oil Palm genome sequencing using paired-end and mate-pair libraries for de novo assembly – Dr Jared Ordway, Orion Genomics, St. Louis, MO, USA

• mRNA-seq and genome sequence capture – Professor Jozef Gecz, Women’s and Children’s Hospital, Adelaide

• Coral transcriptomics (mRNA-seq) – Professor David Miller, James Cook University, Townsville, Queensland

• ChIP-seq mapping the Transcription Factor UBF - Dr Ross Hannan, Peter MacCallum Cancer Centre, Melbourne, Victoria

• shRNA library analysis in cancer research - Dr Patrick Humbert, Peter MacCallum Cancer Centre, Melbourne, Victoria

• Sequencing and Assembly of Animal Virus Genome - Dr Thiru Vanniasinkam, Charles Sturt University



Small RNA sequencing for discovery

 "We have been delighted with the quality of the service and the quality of results provided by GeneWorks in relation to small RNA sequencing."

John Mattick
Professor of Molecular Biology & ARC Federation Fellow
Institute for Molecular Bioscience
The University of Queensland

John Mattick

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DeepCAGE analysis of transcription

 "We used GeneWorks to perform DeepCAGE Sequencing of RNA. We have been very pleased with the excellent service provided by GeneWorks and the quality of the CAGE-seq data. Using this data we are able to identify the starts of transcription, confirming known transcription start sites, and importantly, able to identify novel transcripts. Coupled with RNA-seq data, CAGE-seq data can be used to validate the starts of transcription, particularly of lowly transcribed transcripts."


Dr Clare Stirzaker
Epigenetics Research Group, Cancer Program
Garvan Institute of Medical Research
Darlington NSW Australia

Clare Stirzaker

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Oil Palm genome sequencing using paired-end and mate-pair libraries for de novo assembly

"We have been exceptionally pleased with the outcome of our interactions with GeneWorks. This work included next-generation whole genome sequencing utilizing various Illumina paired-end and mate-pair libraries. GeneWorks was open to tailoring the project to meet our specific needs, and the turn-around from the start of the project to the delivery of data not only met our tight timelines, but also exceeded our coverage goals."

Dr Jared Ordway, Ph.D.
Vice President, Research & Development
Orion Genomics
St Louis, MO 63108, USA



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mRNA-seq and genome sequence capture 

"GeneWorks have been fantastic in helping us to embrace the new technologies of RNA sequencing and genome partitioning and next generation sequencing by providing excellent service and expert support. I greatly appreciate their enthusiasm, efficiency and timely response, all of which helped us significantly to achieve our goals. Great service and a great experience overall."

Prof Jozef GECZ, PhD
NH&MRC Principal Research Fellow
Head, Neurogenetics, Genetics and Molecular Pathology
Women’s and Children’s Hospital, Adelaide, SA, Australia

Jozef Gecz

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Acropora millepora
Photo courtesy of Zoe Richards

Coral transcriptomics

"Our work has focussed on the staghorn coral Acropora millepora as both a model organism for coral biology, and as a comparitor for understanding the evolution of animal genomes. This is possible because corals are anthozoan cnidarians - they are amongst the most morphologically simple of “true” animals, but are remarkably vertebrate-like in terms of gene content. In 2001 we began an EST project on A. millepora, and this has evolved into an attempt to assemble the “complete” transcriptome. For this purpose, we are using about 20,000 (Sanger) ESTs and several plates of 454 data, supplemented with three lanes of Illumina data run on a GeneWorks GAII. The aim with these runs was not only transcriptome assembly, but also to use the data to follow changes in the transcriptome during early coral development.

We made three paired-end libraries from different developmental stages using the mRNA seq kit. GeneWorks were really helpful throughout the library making process, providing advice and feedback on controls etc, and the process was very efficient. GeneWorks were particularly helpful in attempting to resolve problems that arose in the data analysis pipeline.

The data were high quality and the volume generated was enormous – an average of about 9 million reads per lane, yielding approximately 1.4 GB per lane. In addition to the cost-effectiveness of this approach relative to other high throughput methods, statistics that really surprised (and impressed us) were that two lanes of Illumina data yield a transcriptome assembly comparable to that generated from a full plate of 454 data, but with substantially more long contigs (for size classes above 3kb Illumina outperformed 454, despite the Illumina data being 75bp reads). Moreover, the contigs were of remarkably good quality.

Our experience in dealing with Illumina data has led us to reevaluate the original intention of printing oligonucleotide arrays for gene expression analysis - we now hope to use the GAIIx rather than arrays."

Prof David J Miller
Comparative Genomics Centre and
ARC Centre of Excellence for Coral Reef Studies
James Cook University

David J Miller

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ChIP-seq mapping the Transcription Factor UBF

"We used GeneWorks’ services for a recent ChIP-seq project, our first venture into next gen sequencing. GeneWorks helped by clearly explained the options, picked up our ChIP samples and had data back to us within a month. We found GeneWorks professional and easy to deal with and were impressed by the volume and quality of the data.

Research application: Chromatin immunoprecipitation (ChIP) -sequencing analysis was performed to examine the specific localisation and enrichment of cytoarchitectural Polymerase I transcription factor, UBF, on the ribosomal rRNA gene repeats in mouse fibroblasts. Total fragmented genomic DNA as well as DNA fragments cross-linked to UBF and isolated by immunoprecipitation were sequenced using the Illumina Genome Analyser system (GeneWorks). All sequences were mapped to the published complete sequence of the mouse rDNA repeat." 

Dr Ross Hannan
Peter MacCallum Cancer Centre


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shRNA library analysis in cancer research

"We chose GeneWorks as our partner for the next gen sequencing component of a ground-breaking shRNA library-based approach to studying tumour suppressive functions of key genes. In the design phase GeneWorks helped us understand the way the Genome Analyzer technology worked. Their sequencing service was efficient and extremely fast and we found their staff helpful and well informed. We received our set of high quality data back within two weeks of them picking up our sample."

Dr Patrick Humbert
Peter MacCallum Cancer Centre


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 Sequencing and Assembly of Animal Virus Genome

"Geneworks did a great job in helping us determine the sequence of a virus. The level of service provided was outstanding and I look forward to undertaking more DNA sequencing with GeneWorks in the future"

Dr Thiru Vanniasinkam
Charles Sturt Univerisy


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