UAB Comprehensive Cancer Center (CCC) Microarray Shared Facility

Director:  Jan Dumanski, PhD

Co-Director: Michael R. Crowley, PhD

Department/Center Association:  CCC

Established:  June 2002

Mission

The UAB Comprehensive Cancer Center (CCC) Microarray Shared Facility assists investigators who wish to use Microarray technology to study genetic alterations associated with cancer.

Facility Description

The UAB CCC Microarray Shared Facility is located in room 412 of the Kaul Human Genetics Building. Comprised of 520 square feet of physical laboratory space, the Facility is equipped with the Affymetrix Complete GeneChip Instrument System that includes the GeneChip Scanner 3000 7G, Fluidics Station 450 and the GeneChip Hybridization Oven 640. The Facility also has two dedicated workstations with Affymetrix GeneChip Command Console (AGCC) 1.0, Expression Console and Data Mining Tool 3.0 software for data analysis and visualization.  An Agilent 2100 BioAnalyzer is used for RNA quantitation and quality control. Other equipment such as a Thermo Forma refrigerated tabletop centrifuge with multiple rotors/adapters, microcentrifuges, water baths, and Thermo Forma –86^°C Freezer, is also available for sample storage and processing.

The Facility also comprises the Ultimate Microarray Printer (PriZilla) and two Axon GenePix 4000B scanners for custom made spotted arrays analysis. PriZilla is located in Room 411 of the Kaul Building, which is a dedicated clean room with humidity control. This system uses capillary tubes as printing pins that allow printing from 1536-well plates and also produce many more spots from the same amount of printing liquid as compared to the standard printing systems, which considerably reduces the cost of the arrays. Additionally, it uses the latest state-of-the-art high-speed precision x-y stages and the electronics controlling system to overcome the problems associated with over-shooting and jittering, which have become more significant as high speed and density are required. These features allow us to reliably make small spots, so that the arrays can be printed at high-density (down to below 100 micrometer center-to-center distance between two neighboring spots, depending on the surface chemistry used for printing).

The core of our Facility's data analysis and management systems is the ArrayAssist Enterprise Software (Stratagene) running on a Dell Precision 650 Workstation with 4 CPUs, 4GB RAM, and four 40GB hard drives with a DVD burner.  In addition, the PathwayArchitect software (Stratagene) will help investigators better understand gene lists derived from prior (statistical) analysis by identifying gene interactions and exploring disease and signaling pathways.

Research Information

1. GeneChip Technology allows scientists to reach their research goals by identifying genetic variations associated with disease to discovering new drug targets.  The Facility is equipped with the Affymetrix Complete GeneChip Instrument System and is providing full Affymetrix GeneChip experiment services.  Services include technology consultation, experimental design, RNA isolation, RNA quantification and quality control, target preparation, array scanning, and data extraction and analysis.  The service fees and genechip prices are located at http://www.microarray.uab.edu under Services. 

2. Custom Spotted Arrays offer a lower cost alternative to the Affymetrix system. Spotted arrays utilize a two color system of labeling that many investigators find preferable. At this time we are able to provide custom-made spotted arrays of the 32K BAC set for the human genome. We are exploring the possibility of creating a similar genomic array for the two most commonly used mouse strains, C57/Bl6 and 129/Sv using the Ultimate Array Printer (PriZilla) constructed by the Bioinstrumentation group at Lawrence Berkeley National Laboratory and brought to UAB by Dr. Dumanski. Please contact Dr. Carl Bruder of the Microarray Printing Facility for more information on custom spotted arrays (cbruder@genetics.uab.edu).

3. Bioinformatics Resources provide up-to-date data analysis software packages that store, analyze, visualize, annotate, and report on the data from both Affymetrix GeneChip and spotted arrays.  The new feature of ArrayAssist Enterprise software will enable investigators to analyze their data through a Web-based interface.

Contact Information

Director:  Jan Dumanski, PhD

Email: jdumanski@uab.edu

Phone:  205-996-4055

Co-Director:  Michael R. Crowley, PhD

Email:  mcrowley@uab.edu

Phone:  205-975-2013

Web Site:  http://www.microarray.uab.edu/

Approved by: Jan Dumanski, PhD, Director and Michael R. Crowley, PhD, Co-Director

Date: February 22, 2008.

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