Program in Bioinformatics & Proteomics/Genomics : Genomics Core Lab - Services

	Genomics

These services are provided by the Genomics Core Laboratory:

Affymetrix Microarray Analysis

The GCL performs gene expression analyses with the Affymetrix GeneChip system. Standard Affymetrix protocols are used by the investigator to prepare biotin-labeled cRNA starting from either total RNA or mRNA. At present, the GCL can accept only prepared biotin-labeled, fragmented cRNA samples, and carries out hybridization of the prepared samples, post-hybridization washing and staining, and scanning of fluorescence levels utilizing a GeneArray™ scanner. RNA isolation and fragmented target cRNA preparation services should be available in the near future.

The most commonly used Affymetrix GeneChip® arrays are: Human (GeneChip® Human Genome U133 Plus 2.0 Array analyzes expression levels of over 47,000 transcripts and variants, including 38,500 well-characterized human genes), Mouse (GeneChip® Mouse Genome 430 2.0 Array analyzes 39,000 transcripts and variants from over 34,000 well-characterized mouse genes), and Rat (GeneChip® Rat Genome 230 2.0 Array analyzes over 30,000 transcripts and variants from over 28,000 well-substantiated rat genes). The Human, Mouse, and Rat GeneChips cost approximately $525 per chip and are ordered by the customer (please contact us prior to placing an order). Other Affymetrix genome arrays are available for a number of organisms. The processing cost for each sample covers chip hybridization and scanning, and preliminary data analysis.

We strongly encourage users to consult with us on the planning of their GeneChip experiments. We will gladly offer our advice in the experimental design, choice of chips, sample preparation, and coordination of experiment timings.  You can contact the GCL Director by e-mail or by phone: David Weaver, DDS, PhD, 419-383-6105. He is also happy to speak to your research team or department about the GCL and microarray analysis.

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Hybridized slides can be brought back to the GCL to be scanned. Slides are scanned by a PerkinElmer ScanArray Express Microarray Analysis System that uses 543 nm and 633 nm lasers for excitation intensities of the labeled hybridized samples. PerkinElmer™ QuantArray Microarray Analysis software is used for image analysis, and the GCL staff will assist researchers in its use.

If you would like to design a custom microarray project, please contact the GCL Director by e-mail David.Weaver@utoledo.edu or by phone: David Weaver, DDS, PhD, 419-383-6105. He is also happy to speak to your research team or department about the GCL and microarray analysis.