McMaster University

Centre for
Functional Genomics

Scope of Search


The Waller Family Gene Array Facility

Affymetrix Service

Welcome to the McMaster University Gene Array Facility. We offer Affymetrix oligonucleotide arrays for expression quantification, regulation and whole genome DNA analysis. Our microarray service can currently process:

  • GeneChip Expression Arrays
  • GeneChip Exon Arrays
  • Genome-wide Human SNP and Mapping Arrays

The Gene Array Facility also provides software tools for data management and analysis covering all respective fields of functional genomics. The Affymetrix Service is available to all academic and commercial laboratories in Ontario and beyond.


The Gene Arrays Facility also provides a four-laser AXON GenePix 4200A scanner (Molecular devices) for scanning of commercial and custom-arrayed cDNA, protein and tissue microarrays. The AXON system includes Molecular Devices Acuity 4.0 Software for mining and analysis of GenePix format specific microarray data.

Agilent Bioanalyzer

The Agilent 2100 bioanalyzer is the standard for RNA sample QC, DNA fragment analysis and SDS-PAGE analysis of protein samples. A unique feature of the Agilent 2100 bioanalyzer is that it can be used for both electrophoretic separation and flow cytometric analysis of cell fluorescence parameters. The Bioanalyzer is routinely used for monitoring the quality of total, IVT and fragmented RNA in one and two cycle 3’ target labeling assays.

Applied Biosystems TaqMan

The 7900HT Fast Real-Time PCR System is a real-time quantitative PCR system that combines 384-well plate compatibility with fully automated robotic loading for Gene Expression and SNP Genotyping assays. Acknowledged as the gold standard in real-time PCR, the 7900HT system combined with TaqMan® Genomic Assays enables one to achieve unprecedented throughput and flexibility as well as pursue projects beyond the scope of previous real-time instruments.

Light Cycler (Roche Applied Science)

The LightCycler System offers solutions for flexible real-time PCR quantification, mutation analysis and SNP genotyping. The instrument has enhanced sensitivity compared to the TaqMan system being able to detect a single copy gene in one genome equivalent of DNA.

Bio-Plex System (Bio-Rad Laboratories)

The Bio-Plex system is a flow-based suspension array system for simultaneously identifying and quantitating up to 100 different analytes in a single biomolecular assay. The system measures molecules bound to the surface of fluorescent microspheres, providing highly accurate, real-time digital analysis of serum or culture media as small as 50 ul. The Bio-Plex system allows for quantitative analysis of a wide variety of cell biology assays, including immunoassays, complex genetic assays and enzyme assays.

Custom Arraying

The Gene Array Centre is equipped with a BioRad VersArray Chip Writer Pro system for custom printing of cDNA, proteins, macrophage libraries. The instrument arrays biological samples from 96-well or 384-well source plates onto glass slides or membranes. Microarray spotting configuration allows printing >57,000 spots per slide while membrane gridding configuration can print nearly 25,000 spots per membrane using 48 pins. Capacity is up to 24 slides, including 4 blot slits.