Genomics encompasses extraction, genotyping, sequencing and other genomics-related services across a range of University of Queensland facilities.
Australian Centre for Ecogenomics (ACE) Sequencing
Services
- DNA extraction
- Quantitative PCR
- Amplicon sequencing and community profiling
- Metagenomics
- Metatranscriptomics and RNA sequencing
- Single Cell Genome Analysis
- Oxford Nanopore long read sequencing
- Microbial bioinformatics
Equipment
- Illumina NextSeq500
- Illumina MiSeq
- Oxford Nanopore MinION
- Oxford Nanopore PromethION
Contact
Ms Janette Edson, Sequencing Manager
School of Chemistry and Molecular Biosciences
(07) 3365 4318
ace_sequencing@uq.edu.au
Australian Genome Research Facility (AGRF)
Services
The Australian Genome Research Facility (AGRF) is a key enabler of world-class genomic science and offers a range of services covering all aspects of genomics. Services include: Next Generation Sequencing, Microbial Diversity Profiling, Genotyping, Genetic ID, Long Read Sequencing, Sanger Sequencing, Gene Expression, Bioinformatics and Nucleic Acid Extraction
Equipment
- Illumina NovaSeq 6000
- Illumina NextSeq 500
- Illumina MiSeq
- PacBio Sequel II
- Agena MassArray
- Illumina iScan
Contact
Saurabh Shrivastava
Australian Genome Research Facility
(07) 3365 8815
saurabh.shrivastava@agrf.org.au
AGRF Ltd Gehrmann Laboratories Research Road University of Queensland Qld 4072
AGRF-UQ PacBio Service
Services
Equipment
- PacBio Sequel II
Contact
AGRF Brisbane Node Manager
Dr David Hawkes
(07) 3346 9682
Gehrmann Laboratories, Gehrmann Building 60, Research Road, St Lucia campus
Genetic Research Services (GRS)
Genetic Research Services (GRS) provide high-quality genetics services to both UQ and external clients. Backed by a multi-disciplinary team and state-of-the-art equipment, we offer a number of services to support your research needs.
Expertise
- Rodent genotyping service - We genotype all types of genetic modifications including knockouts, knockins, conditional/floxed, transgenes, SNPs, and CRISPR. The service includes genotyping assay design, DNA extraction, and fluorescent PCR coupled with capillary electrophoresis for highly accurate and sensitive detection of assay products. The genotyping results are analysed by a team of highly experienced research staff.
- Sequencing – We offer high quality, fast, customised services for sequencing clients. We also provide customised solutions and specialised customer support for troubleshooting undesirable results and offer different sequencing dyes (v3.1 and v1.1) for particularly difficult DNA templated eg. hairpin or highly repetitive regions. The Sanger DNA sequencing service is performed on our two 3730 Applied Biosystems capillary electrophoresis machines.
- Fragment Services - Our fragment analysis service can speed up your research by analysing your PCR results in a 96-well plate format using high-throughput CE DNA analysers. Fluorescently labelled PCR products from 50-1100 base pairs can be analysed and differences in fragment size as little as 1 base pair can be detected. PCR assays are commonly used to screen for the presence or absence of a variety of genetic features, e.g. insertions, deletions, and SNPs, in a range of organisms. These assays include techniques such as:
- Restriction Fragment Length Polymorphisms (RFLPs)
- Amplified Fragment Length Polymorphisms (AFLPs)
- Single-stranded conformation polymorphism (SSCPs)
- Other custom designed PCRs
- Robotics Services – We have a number of automated robotic instruments for laboratory work (pre and post PCR), PCR machines and 3730 DNA analysers that may assist you with your high throughput laboratory needs. PCR automation and automated processing reduces the risks of injury, errors, and time associated with the manual processing of high numbers of samples within the laboratory. We can help with automating DNA extraction, PCR, and PCR set up and plate preparation.
- Microsatellite/STR Panels - We can optimise microsatellite panels, perform capillary separation, and analyse the results for a variety of animals including but not limited to horses, sharks, and manta rays.
- SNaPshot Multiplex SNP Detection – We can detect up to 10 SNPs simultaneously using the SNaPshot multiplexing method available from Applied Biosystems. This method allows for rapid screening of a panel of SNPs in a high number of samples for projects such as population genetics and profiling.
- Bacterial 16S Testing - Our bacterial 16S test detects the presence of the 16S ribosomal subunit gene which is highly conserved in the genomes of many different strains of bacteria. This test can be useful for applications such as detection of bacterial contamination in faecal samples from germ-free mice in gnotobiotic facilities and for monitoring of sterile environments. Positive 16S results can also be investigated to try and identify the bacterial strain via further 16S sequencing and comparison to online databases.
Contact
Manager, Ms Leanne Clarke
(07) 3365 1739
Genome Innovation Hub (GIH)
Genome Innovation Hub (GIH) is a University of Queensland initiative and is part of UQ Research Infrastructure. GIH aims to develop innovative approaches to advance technologies in structural and functional analysis of genomes. The innovation hub acts as a collaborative research centre, working with UQ clinicians and scientists to implement novel and promising methodologies in projects focussed on the key areas of health, agriculture and the environment.
Genomic expertise
- Single-cell sequencing and library preparation
- Long read sequencing
- Protein engineering and purification
- Genome editing and manipulation
- Spatial transcriptomics and advanced imaging
- Bioinformatic assembly of complex genomes
- Transcriptomics
- High throughput genetic screening platforms
- Computational tool development for analysis of genomic and transcriptomic data
- DNA and RNA extraction from difficult sources
- Microfluidic partitioning and barcoding for single-cell analysis
Contact
Operations Manager
Stacey Andersen
(07) 3346 2607
Institute of Molecular Biosciences, IMB Building 76, St Lucia campus
UQ Sequencing Facility
Services
Standard library preparation and sequencing services include
- Illumina (short read) whole transcriptome sequencing for gene expression profiling or deeper transcriptome analysis
- 10x Genomics Chromium Single Cell 3' Gene Expression (including CITE-seq/cell hashing)
- PacBio whole genome sequencing (long reads and HiFi reads)
- PacBio IsoSeq (full length transcript analysis)
In addition, we are happy to discuss how we can help with your custom sequencing requirements. We have experience with library prep and/or sequencing in the following areas:
- Exome and custom capture
- Illumina sequencing panel
- Amplicon sequencing
- Sequencing customer-prepared libraries
- 10x Genomics Chromium VDJ and Single Cell ATAC assays
- Spatial transcriptomics
- ATAC-seq
- CAGE
- Small RNA
- Hi-C
RNA and DNA Quality Control
- Agilent Bioanalyser
- LabChip GX Touch
- Invitrogen Qubit
Equipment
- Illumina NextSeq 500 platform
- Illumina MiSeq platform
- 10X Genomics Chromium Single Cell system
- PacBio Sequel II
Contact
Angelika Christ, Dr Tim Bruxner or Shivangi Wani
Institute for Molecular Biosciences
(07) 3346 2074
Institute of Molecular Biosciences, IMB Building 76, St Lucia campus
Queensland Facility for Advanced Genome Editing (QFAGE)
Services
Cell and animal model CRISPR genome editing
- Gene knock-out
- Large fragment deletion
- Knock-in (SNP, reporter, floxp, etc. )
Cell line engineering - Generation of stable expression cell lines using
- Safe harbour locus CRISPR knock-in
- Piggybac transposon system
Lentiviral particle production
- High titers of ≥ 108 TU/ml (transducing unit per ml) – only for UQ-wide community
Other cell line service
- CRISPR and Transfection optimisation
- Karyotyping
- Mycoplasma testing
- Genotyping and CRISPR analysis
Equipment
- Neon electroporation system - Thermo Fisher Scientific Neon
- 4D Nucleofector System - Lonza (shared by Genome Innovation Hub)
- Countess II FL Automated Cell Counter - Thermo Fisher Scientific (shared by Genome Innovation Hub)
Contact
Dr Xiaoli Chen
Queensland Facility for Advanced Genome Editing (QFAGE)
(07) 3346 2348
Institute for Molecular Bioscience, Queensland Bioscience Precinct (Building 80)
Real Time Polymerase Chain Reaction (qPCR)
Services
Quantitative "real time" PCR (qPCR) instruments measure the accumulation of signal generated by fluorescent dyes during each cycle of PCR. SCMB qPCR facility offers a range of instrumentation for qPCR set up, data acquisition and data analysis. We provide training, instruments, lab ware, SYBR reagent and working space, just bring your samples.
Equipment
- AB-QuanStudio 6 qPCR machine: 6-colours (green to far-red), 384-well plate block, QantStudio software. SYBR and TaqMan compatible.
- AB-Viia7 qPCR machine: 6-colours (green to far-red), 384-well plate block, QantStudio software. SYBR and TaqMan compatible.
- QIAGEN –Rotor-Gene-Q qPCR machine: 72-tubes rotor, 2 colours (green 470Em/510Em and yellow - 530Ex/557Em)
- Eppendorf epMotion 5075/5073 pipetting robotics system
- Integra AssistPlus pipetting robot with Viafo and Voyager electronic 8- or 12- channel pipettes
- Laminar-flow hood, multichannel pipets and plastic ware for manual PCR stet up
- Maxwell16 DNA/RNA/Protein isolation robot
- QBIT-4 fluorometer for fast and sensitive quantification of DNA, RNA, and Protein
Contact
Dr Vitaliya Sagulenko
School of Chemistry and Molecular Biosciences
(07) 3346 7539/ 0409 132 834
- Analytical and environmental
- Biological resources
- Computation
- Crystallography
- Flow cytometry
- Genomics
- Histology
- Humanities and Business
- Hypersonics
- Imaging
- Mass Spectrometry
- Materials and Fabrication
- Microscopy
- Microwave Engineering and Photonics
- Mining and minerals processing
- Nanofabrication
- Nuclear magnetic resonance (NMR)
- Recombinant protein production
- Research Stations
- Spectroscopy
Get in touch
For general information about UQ's equipment and infrastructure, contact the Director, Research Infrastructure.
(07) 3443 1033