Atlantic Microarray FacilityInstitut de recherche médicale Beauséjour - Beauséjour Medical Research Institute
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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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