Equipment
The PolyPlex
2 Oligonucleotide synthesizer is a fast, high throughput
instrument capable of making 96 oligo’s (DNA or RNA)
simultaneously. With a cycle time of 10 minutes, a plate of
25-mers (for example) is ready in about 4 hours.
Below: A typical example of the high DNA oligomer quality
as analyzed by electospray mass spectrometry.
The OmniGrid
100 Microarrayer uses a 48-pin capable printhead and Telechem
Stealth contact printing pins. Up to 100 slides can be
printed with biological samples in one production batch. The
integral Server Arm 3 robot automatically handles up to 72
plates (96 and 384 plates are most common) in a humidity controlled
chamber.
Below: An example of the AMF 18K Human Oligo Chip. This chip is also used
in breast cancer research at the Beauséjour Medical Research Institute
(BMRI).

Below: Our Axon Instruments GenePix 4000B microarray scanner achieves 5 μm resolution from two lasers at 532nm and 635nm wavelengths.

Below: The Precision
2000 liquid handling robot for 96-96, 96-384 and 384-384
transfers. Used in the preparation of print source 384-plates
for microarray printing.
Other Equipment at the Atlantic
Microarray Facility, Beauséjour Medical Research Institute
- Syngene ChemiGenius
2 image acquisition system
- ThermoSavant SPD SpeedVac and UVS400 Universal Vacuum System
- Molecular Devices SpectraMax 384Plus platereading spectrophotometer
- Perkin-Elmer and Eppendorf PCR lab.
- Cepheid SmartCycler II RT-PCR
BIOINFORMATICS
Here is a list of the software and databases that we have
found to be useful to date:
Software
Sequence Design: ArrayDesigner 3.0 (Premier Biosoft); In-house made Bioperl
software
Preprocessing: GenePix Pro 5.0 (Axon Instr.); SpotReader (Niles Scientific)
Database and analysis: Acuity 3.0 (Axon Instr.)
Data Analysis: Bioconductor (www.bioconductor.org);
TMeV (www.tigr.org); BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html);
and many other freeware software for specific tasks.
Pathway analysis: GenMapp (http://www.genmapp.org/MAPPFinder.html)
Databases
RefSeq is used for sequence design and sequence identities for
the AMF Human Oligo 15K chip
Isoform chips are designed from the Ensembl database (exon information) and in-house
made Bioperl software (using sim4)
Salmon chip designed using sequences from Genomic Research on Atlantic Salmon
Project consortium information (http://web.uvic.ca/cbr/grasp/)
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