Genomics
Capabilities
The LIMS Genomics Facility provides investigators with the latest in "next generation sequencing" equipment to facilitate wide-ranging research projects requiring highly detailed global DNA and RNA sequence analysis. Facility capabilities include:
- whole genome and transcriptome sequencing
- targeted re-sequencing of PCR amplicons and exomes
- epigenomic analyses of DNA methylation, microRNA expression patterns and DNA-protein interactions
- sequencing library preparation
- automated microchip electrophoresis and quantification of small quantities of nucleic acid (e.g. amenable to laser capture micro-dissected tissue specimens).
Equipment
Large scale nucleic acid sequencing
Illumina HiSeq 1500
Applications:
- Large scale DNA sequencing capacity (60-300 Gb)
- De novo genome sequencing (unknown genomes)
- Targeted resequencing - multiplexed PCR amplicons > exomes > known genomes
- Transcriptome (RNA) sequencing (identify and quantify global mRNA expression patterns
- Global analysis of DNA-protein interactions using ChIP-seq
- Identification and quantification of micro RNAs without prior genome annotation
- Genotyping by sequencing (RADseq)
- Epigenetic sequencing of:
-
- bisulfite-converted DNA
- methylation-sensitive restriction digest-enriched fragments
- anti-methyl C-precipitated fragments
- chromatin IP of methyltransferases containing aza-labelled DNA.
Small scale sequencing
Illumina MiSeq Personal Sequencer
Applications:
- Small to medium scale sequencing capacity (<8 Gb)
- De novo genome sequencing of small to medium sized genomes
- Exome sequencing
- Transcriptome sequencing
- Genotyping by sequencing (RADseq)
- Targeted re-sequencing (e.g. sequencing of disease-associated genes in a patient cohort)
Sequencing library preparation and QC
Shimadzu MultiNA Microchip Electrophoresis System
Applications:
- Automated microchip electrophoresis and quantification of nucleic acids
- DNA size and quantitative analysis
- Analysis of PCR products and restriction digests
- mRNA expression and transcriptome analysis
- Quality check of in vitro synthesised mRNA
- Purity check of RNA extracted from tissues and cells
Sage Science Pippin Prep
Applications:
- automated DNA size selection and purification
- collects targets between 50-1500 bp
Diagenode Bioruptor and Covaris AFA ultrasonicator
Applications:
- unbiased fragmentation of DNA/RNA
- chromatin shearing for ChIP
Contact
For more information about accessing the LIMS Genomics Facility, please contact:
Dr Stephen R. Doyle
T: +61 3 9479 3087
E: S.Doyle@latrobe.edu.au
