Hudson Genomics
Established at Hudson Institute of Medical Research and located at the Monash Medical Centre in Clayton Victoria, Hudson Genomics services our precinct partners; Hudson Institute, Monash University and Monash Health, as well as the wider Victorian and National scientific community.
Hudson Genomics provides a comprehensive range of genomic technologies and expertise to accelerate research and clinical diagnosis. A commitment to quality and client support is paramount to our services.
Contact us
General Enquiries
e: genomics@hudson.org.au
Dr Trevor Wilson | Scientific Manager
t: +61 3 8572 2818
Jodee Gould | NGS Specialist
t: +61 3 8572 2462
Anh Vo | NGS Specialist
Our Services
Gene Expression Services
qPCR Resources
The facility hosts two Applied Biosystems Quantstudio™ 6 -384 block instruments.
The instruments support SYBR®, Taqman®, standard and fast chemistry and allow 5 colour multiplexing.
Services
- Instrument booking (iLabs) – (Hudson Institute, Monash University users only).
- Training is required for Quantstudio access and use. Please contact genomics@hudson.org.au
Applications
- Gene/miRNA Expression
- Genotyping
- Copy Number Variation
- Protein Thermal Shift
- High-Resolution Melt
- Pathogen Detection
Resources
- QuantStudio 6 manual
- DataAssist™ Software
- Real-Time PCR Troubleshooting Tool
- Real-Time PCR Systems Chemistry Guide
- Sigma qPCR Technical Guide
- Relative Quantitation Using Comparative Ct Getting Started Guide
- Absolute Quantitation Using Standard Curve Getting Started Guide
- Allelic Discrimination Getting Started Guide
- Understanding Curves
Biomark
The Biomark™ HD system is the industry-leading high-throughput real-time PCR instrument.
It enables multiplex qPCR quantitation to determine gene expression levels in multiple samples simultaneously, without the need to run multiple plates. It is useful for studies where many samples need to be screen for multiple targets or for validation studies, where multiple samples can be screened against up to 192 different targets.
Services
- Please contact genomics@hudson.org.au requesting an initial consultation for your Biomark™ HD project.
- Upon quotation acceptance, please submit your samples according to our sample submission guidelines.
Taqman Assay Library
The facility has purchased many Taqman Assays and thus now has a Library (Human and Mouse) of assays focused primarily on infection and immunity, regenerative medicine, biomarkers and drug discovery markers. Often it is possible to screen some genes of interest without purchase of assays.
Sample submission
- Follow the Biomark Gene Expression Sample Submission Guide.
- 6 µl of cDNA (10-100 ng/µl) suspended in nuclease-free water or TE buffer
Data Retrieval
- Data Retrieval is by Cloudstor
- Data is processed by Fluidigm Real-Time PCR analysis software
- A quality report will then be provided detailing methodologies for publications
Next Generation Sequencing (NGS)
Next Generation Sequencing (NGS) utilises massively parallel sequencing to generate thousands of megabases of sequence information per day. Our NGS service utilises the latest Illumina Sequencing Instruments including NextSeq2000, NextSeq550 and MiSeq, providing speed, flexibility and versatility for your project. We undertake both library generation and next generation sequencing as required.
Services
- Please email the facility genomics@hudson.org.au requesting an initial consultation for your NGS project design. Once the design is discussed and finalised, a quotation will be emailed to you.
- We also suggest that you have discussions with your bioinformatician or the Monash Bioinformatics Platform before finalising experimental design.
Sequencing Library preparation
- The facility prepares sequencing ready libraries using a wide range of both commercial kits and in-house protocols. These include processing low quality (eg; FFPE) and low quantity (eg; sorted cells) samples. Please contact the facility to discuss your requirements.
- Current library preparations include:
- pA RNA-Seq
- Ribodepletion RNA-Seq
- Metatranscriptomes
- 3’pA RNA-Seq
- WGS libraries
- Metagenome libraries
- Amplicons
- ChIP-Seq libraries
- WES libraries
- Targeted panels (e.g. TSO500)
Further details about RNA-Seq analysis
Sequencing
We can prepare libraries and sequence them; or we can sequence researcher prepared libraries. The Genomics facility currently performs sequencing on 3 different Illumina instruments; The NextSeq2000, NextSeq550 and MiSeq. Please contact the facility to discuss the best option for your project.
-
- NextSeq2000
- P1 chip ~100 Million Reads/Read Pairs
- P2 chip ~400 Million Reads/Read Pairs
- P3 chip ~1100 Million Reads/Read Pairs
- Available in different formats from 50nt Single End to 300nt Paired End depending upon chip
- NextSeq550
- 130 or 400 million reads/read pairs with 75 single End to 150nt Paired End
- MiSeq
- 1-25million reads/read pairs, up to 300nt paired end
- NextSeq2000
Sample submission
- Firstly, please discuss exactly what is required for submission with facility staff.
- Upon quotation acceptance, please follow the NGS Sample submission guidelines.
- Please submit your samples using the NGS Sample submission form.
Data Retrieval
- Data Retrieval is via our server using the MyTardis system.
- Results will usually take approximately 4 weeks, provided that the samples pass quality control.
- A link to your data will be provided electronically and a quality report will also be provided detailing methodologies used to assist publication. Note that links to data are valid for one month, and although data is archived for longer, it is suggested that you download and securely store your own data.
Agilent Bioanalyser
The Agilent Bioanalyser uses microfluidic technology to perform RNA and DNA electrophoresis for sizing, quantification and quality control. Referenced by more than 10,000 peer-reviewed publications, the Agilent 2100 Bioanalyser with its DNA and RNA kit portfolio has become the industry standard DNA/RNA quality control tool.
Services
- Please contact genomics@hudson.org.au requesting an initial consultation for your project.
RNA analysis
The RNA 6000 Nano kit provides a check of total RNA integrity and quantifies total RNA and mRNA in the low to mid nanogram range.
The RNA 6000 Pico kit provides high sensitivity analysis to quantify low concentrated RNA samples down to 50 pg/µl.
The RNA integrity number (RIN) is a software tool designed to help scientists estimate the integrity of total RNA samples.
DNA analysis
The DNA kits are ideal for automated sizing and quantification of PCR fragments, restriction digests or fragmented DNA
| Kits and Reagents | Samples per chip | Analysis Range |
| RNA 6000 Nano | 12 | total RNA: 30-500 ng/µl , mRNA: 25-250 ng/µl |
| RNA 6000 Pico | 11 | total RNA: 50-5000 pg/µl , mRNA: 250-5000 pg/µl |
| DNA 1000 (25–1000 bp) | 12 | 0.5-50 ng/µl |
| High Sensitivity DNA (50-7000 bp) | 11 | 5-500 pg/µl (up to 10ng/ul for sheared DNA) |
Sample submission
- All samples are submitted using the Agilent Bioanalyser Request Form.
- Submit 2 µl of your sample (0.2 ml tubes) within the specified concentration range for each analysis.
- Refer DNA Kit Specifications
- Refer RNA Kit Specifications
Single Cell Sequencing
Hudson Genomics uses the 10x Genomics Chromium for a variety of single cell genomic assays including:
- 3’ RNA-Seq
- 5’ RNA-Seq
- TCR Sequencing
- BCR Sequencing
- ATAC- Seq
- And a combination of the above
Please contact genomics@hudson.org.au for further information.
Covaris System
The Covaris Adaptive Focused Acoustics™ (AFA) process uses acoustic energy wave packets from a dish-shaped transducer to reproducibly shear DNA fragments to tight size distribution ranges. The Covaris technology enables controlled, quantitative and standardised sample preparation for various applications, including shearing DNA fragments for next generation sequencing library preparation.
The Covaris System is the only system that can successfully and reproducibly shear DNA in the size range of 100-5,000 bp+, eliminating the need for multiple shearing technologies. The process also maintains DNA integrity, as shearing is carried out under temperature-controlled conditions in a closed vessel, which eliminates the risk of cross-contamination.
Covaris support and resources, including applications, how the technology works, protocols, FAQs and publications, are provided at the Covaris website.
Services
- Covaris services are for Hudson Institute and Monash University clients only.
- Training is required prior to using the Covaris instrument.
- Contact the facility genomics@hudson.org.au for Covaris training.
Terms and Conditions
Users of the Hudson Genomics facility are subject to the following Terms and Conditions.
Acknowledging the facility
The Hudson Genomics facility operational expenses are funded through a fee-for-service system. However, for infrastructure, equipment or major technology upgrades, the facility is dependent upon grants from government agencies and the generosity of philanthropic organisations.
To ensure that the facility can clearly demonstrate its critical value and impact to research excellence, we require a visible profile in the research community. The researcher, upon accepting our terms and conditions of service, agrees to acknowledge the Hudson Genomics facility as the service provider in any publication or in any grant application that relates to research undertaken within the facility.
Thank you for your support.
Our Supporters
Established in 1999, the Hudson Genomics Facility is located at Hudson Institute of Medical Research and provides services to our precinct partners; Hudson Institute, Monash University and Monash Health, as well as the wider Victorian and National scientific community.
Hudson Institute is grateful for the generosity of the following supporters who were integral in establishing and contributing to this leading genomics facility.
