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Genomics Core Lab - Introduction
Genomics is the study of the full complement of genes that make up an organism. At
UT, the focus is on which genes are being transcribed (expressed) in different cells
using microarray technology. The Bioinformatics and Proteomics/Genomics Program's
Genomics Core Laboratory (GCL) provides students and researchers with the advanced
analytical tools and approaches needed for state-of-the-art biomedical research.
Microarrays can track tens of thousands of molecular reactions in parallel to detect
specific genes or to measure the activity of genes. The massive amounts of data produced
from these studies require "mining" or the systematic application of statistics to
determine significant findings.
For a complete list of Core Labs at The University of Toledo, please click this link: http://www.utoledo.edu/corelabs/index.html
LOCATION OF GENOMICS CORE LAB in the HEALTH EDUCATION BUILDING
RNA or DNA Microarrays for Your Research Needs
Available at the GCL, the Affymetrix GeneChip system utilizes Affymetrix GeneChip Expression arrays. The PerkinElmer ScanArray 4000 System scans microscope slide-formatted arrays. (See GCL Instrumentation link for more details.)
Make Use of Commercially-Available Protein Microarrays in Your Research
The University of Toledo Genomics Core Laboratory (GCL), on the Health Science Campus has imported the definition files for a variety of commercial protein microarrays (see list below), and can now rapidly and inexpensively scan them and provide the results.
Protein microarrays can be used in many different areas of research, and can be used to do a number of things in addition to straightforward expression profiling. Formats available include proteomic arrays, microspot ELISA and antibody arrays, single-capture antibody arrays, antigen arrays (reverse arrays), microarray westerns and protein binder arrays. To detect proteins bound to arrays, the samples are labeled directly with a fluorophore or a hapten.
The GCL includes a PerkinElmer ScanArray 4000 dual wavelength laser scanner. The scanner reads microscope slide formatted arrays, with separate scans at wavelengths of 633 and 543 nm. Numerous fluorescent dyes are compatible with this system, including Cyanine 5 and Cyanine 3, or Alexa 647 and Alexa 546. The software uses .gal files, provided by the microarray manufacturer, to locate and identify array features.
A number of commercially manufactured peptide and protein microarrays are available for applications such as miniaturizing and multiplexing existing ELISA assays, detecting infections, study of autoimmune diseases, epitope mapping, simultaneous profiling of multiple proteins, biomarker discovery and more. The GCL has successfully tested .gal files from three manufacturers listed below, but we can also read most microarrays from other manufacturers, if a working .gal file of the array is available. Here are some major suppliers:
Arrayit Corporation: http://www.arrayit.com/Products/Protein_Microarrays/protein_microarrays.html
Applied Microarrays, Inc.: http://www.appliedmicroarrays.com/
RayBiotech, Inc.: http://www.raybiotech.com/index.asp
Brief descriptions of protein microarray classes:
Proteomic Arrays
Proteomic arrays are high-density arrays (>1000 elements/array) that are used to identify
novel proteins or protein-protein interactions. The arrays can be created from many
possible sources with the sample to probe the array also coming from many different
sources. One common use is for antibody screening.
Microspot ELISA and Antibody Arrays
These arrays are used for quantitative profiling of protein expression. Usually these
arrays are low density, with known antibodies arrayed to capture antigens from unknown
samples. Detection of bound antigen requires either direct labeling with a fluorophore,
or a second binder/antibody can be used (creating a sandwich assay similar to an ELISA
in a microarray format).
Single-Capture Antibody Arrays
Single-capture antibody arrays consist of multiple known antibodies to profile the
presence of specific antigens from a pooled sample, consisting of both a normal and
disease-associated sample. This type of array uses a direct or hapten label to provide
a qualitative profiling tool to detect binding.
Antigen Arrays or Reverse Arrays
This type of array is normally a low density array (9 to 100 elements) used to investigate
samples for auto-antibodies. The antigen arrays are normally used to profile large
number of samples for the presence of a small number of antigens.
Microarray Westerns
In this array type, samples containing multiple proteins are arrayed and subsequently
probed with a labeled antibody or set of antibodies.
Protein Binder Arrays
Protein arrays are used in this format to identify novel protein binding motifs or
protein-protein interactions. Synthetic proteins or peptides with various binding
motifs are arrayed on the slide surface and are then probed with complex protein mixtures.
Detection with a known antibody allows the user to identify previously unknown binding
events.
To discuss your microarray needs and questions, contact:
David A. Weaver, D.D.S., Ph.D.
Director, Genomics Core Laboratory
Program in Bioinformatics and
Proteomics/Genomics
University of Toledo Health Science Campus
Health Education Building, Room 200
3100 Transverse Drive, Toledo, OH 43614
Phone: 419-383-6105, Fax: 419-383-3251
Email: david.weaver@utoledo.edu
Suggested Readings: Suggested Sites:
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Awards Received/Studies Being Conducted by Investigators Collaborating
with the Genomics Core Laboratory
Determinants of Housekeeping Gene mRNA Levels
David Allison, MD, PhD, Professor, Dept. of Surgery
Dr. Allison began utilizing the Genomics Core Lab for this
project in November 2010. The study is on-going.
NCI - National Cancer Institute (5R01 CA098141-02)
Principal Investigator: Cynthia Smas
Project Title: bHLH Transcription Factors in Prostate Cancer Malignancy
Project Period: July 2003-June 2008
Amount Awarded: $178,000
AHA - NAT - American Heart Association - National (SDG-0335148N)
Principal Investigator: R. Mark Wooten
Project Title: Immunologic Control of Borrelia burgdorferi in Mammalian Tissues
Project Period: 2003-2007
NIAID - National Institute of Allergy and Infectious Diseases (5 R01 AI19149-18)
Principal Investigator: Garry Cole
Project Title: Immunoreactive Macromolecules of Coccidioides Cell Types
Project Period: 1986-2007
Duane Stranahan Charitable Lead Trust
Principal Investigators: Robert Blumenthal and David Weaver
Project Title: Pilot Studies for Affymetrix Microarray Analysis (funds 5 pilot studies
by MUO faculty)
Project Period: March 2005-Feb. 2006
Amount Awarded: $25,000
NIDDK - National Institute of Diabetes, Digestive and Kidney Diseases (1 R21 DK066055-02)
Principal Investigator: Cynthia Smas
Project Title: Functional Analysis of SMAF-1, an Obesity Candidate Gene
Project Period: June 2004-March 2006
Amount Awarded: $100,000
NIGMS - National Institute of General Medical Sciences (5 R01 GM64765-03)
Project Title: AAV, Helper Virus and Host Cell Interactions
Project Period: July 2002-June 2006
Amount Awarded: $205,312
National Institutes of Health (R01 HL68994)
Principal Investigator: George Cicila
Project Title: Identifying Chromosome 3 Blood Pressure QTL Candidates
Project Period: 2001-2006
NIDDK - National Institute of Diabetes, Digestive and Kidney Diseases (5 R21 DK064992-02)
Principal Investigator: Cynthia Smas
Project Title: Molecular Dissection of Regional Adiposity
Project Period: July 2003-June 2005
Amount Awarded: $100,000
National Institutes of Health (R01 HL67276)
Principal Investigator: George Cicila
Project Title: Aerobic Running Capacity QTLs and Cardiac Performance
Project Period: 2001-2005
