Metabolic Research Unit - MRU
The discovery phase aims to identify novel protein targets involved in diabetes, obesity, depression and anxiety utilising state-of-the-art DNA or RNA analysis facilities.
DNA Analysis Facilities
- Configured separately for DNA sequencing and micro-satellite marker genotyping
- Capable of generating 184,000 bases/day and 7,700 markers/day in a single unattended run
- throughput of over 15,000 SNPs/day
- system controlled and data analysed by five networked computers and workstations
Statistical Analysis and Fine Mapping for Disease Genes
Bio-informatics and online database searching provide annotation for ranking our candidate gene list in the target region. The genes and putative regulatory regions are then resequenced for novel variant discovery, and both in silico and novel SNPs typed in our populations. The variants are tested for their influence on the quantitative trait to identify candidate disease genes and verified within our eXpress technology platform for physiological effects.
RNA Analysis Facilities
cDNA Microarray Facilities
We have established a complete cDNA microarray fabrication facility as a key component in gene discovery efforts in the eXpress Technology Platform. This facility consists of:
- Virtek Colony Arrayer
- Qiagen Biorobot 3000
- Virtek ChipWriter Pro microarray robot
- Agilent Bioanalyzer 2100
- Scanarray Lite confocal fluorescent microarray scanner
- Axon GenePix 4000B microarray scanner.
cDNA microarrays derived from cDNA libraries
cDNA libraries from a range of species using tissues that are important to diseases such as obesity, diabetes and depression.
- a source of clones for cDNA microarray fabrication
- 5 libraries comprised of over 12,000 elements - a mixture of known, sequence verified genes and clones derived from these libraries
- Insulin Resistance Gene Chip (IRGC) comprised of over 200 human genes known to be important to metabolism. When coupled with an array of unknown genes, will help identify novel genes exhibiting similar expression patterns to known genes
- Capability of producing custom-designed chips on request
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Israeli Sand Rat |
Hypothalamus |
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Skeletal muscle |
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Human |
Insulin Resistance Gene Chip |
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Skeletal muscle |
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Mouse |
Skeletal muscle |
Data Analysis
Microarray data is extracted from the scanned images using commercial image analysis softwares - GenePix 4 (Axon) or Imagene 5 (BioDiscovery)
Data is assembled as an experimental database and analysed using a range of multivariate statistical analyses, such as Acuity 2 (Axon) or GeneSight 3.2 (BioDiscovery)
Genes with similar expression patterns are identified via grouping strategies such as Hierarchical and K-means clustering and Self Organizing Maps
To reduce the dimensionality of the data, principal component analysis and multidimensional scaling are employed to identify relationships between groups of experimental samples
Target confirmation
Clones are sequence identified. The sequence information is used to generate primers for use in real time quantitative PCR.
Change in expression of the gene of interest is confirmed using an ABI Prism 3700 real time quantitative PCR machine.
Quantitative real time PCR or Taqman analysis use cDNA banks derived from RNA from the original experiment as well as other cDNA sets derived from other experimental cDNA sets.
