McMaster University

Centre for
Functional Genomics

Scope of Search

Gene Chip Expression Arrays

Overview

The GeneChip® expression arrays provide the most comprehensive coverage of the human and various model systems genomes. Expression data from GeneChip arrays can be used for multiple applications including:

  • Discovering new regulatory pathways
  • Validating drug targets
  • Clarifying diseases
  • Analyzing toxicological responses
  • Building robust databases

The Affymetrix arrays utilize 25-mer oligonucleotide probes complimentary to target sequences that are synthesized on the array using photolithography and combinatorial chemistry. Each transcriptional sequence is spanned by 11-20 pairs of oligonucleotide probes randomly spaced throughout the array. All sequences designed on the array are selected from GenBank, dbEST and RefSeq. Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization. Hybridized target cRNA is stained with streptavidin phycoerythrin and arrays are scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570 nm are proportional to the bound target at each oligonucleotides position on the GeneChip® array.

Detailed information about the chips is available from the Affymetrix website.

Academic Price List

The price list contains the current total processing cost per RNA sample including a chip, labeling reagents and 2 or 3 Bioanalyzer chips and related consumables.

Affymetrix GeneChip Price CAD$
Human / Mouse / Rat Gene 1.0 ST Array 600
HG 133 2.0 Plus 850
MOE 430 2.0 850
RAE 230 2.0 820
Arabidopsis ATH1 680
Drosophila 2.0 645
C.elegans 680
Chicken 700
E.coli 2.0 505
Yeast 2.0 680
Xenopus laevis 680
Others Please contact us

Sample Preparation Instructions

For Affymetrix, best results are obtained using 1-5 µg of recently isolated total cellular RNA when using the standard protocol. For samples containing between 10ng and 100ng of RNA, a double amplification protocol could be used. The RNA should be resuspended in commercial RNase-free water (avoid DEPC-treated water). Please do not resuspend your RNA samples in buffers containing SDS or other detergents as these will inhibit the enzyme reaction used to synthesize the probe. We can also extract total RNA from snap-frozen tissues and/or tissues and cells suspended in RNA-later at an additional cost of 20 $ per sample.

Data Transfer

Results from a microarray experiment including *.dat, *cel, *chip and *exp files are sent to the customer via CD/DVD or FTP. For data analysis options, please see the Bioinformatics page.