Program in Bioinformatics & Proteomics/Genomics

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Health Science Campus
Health Education Building & Center for Creative Education Building

BPG Computer Classroom: HEB 1st Floor, Room #127
Genomic Core Lab: HEB 2nd Floor, Room #200

BPG Office: CCE 3rd Floor, Lobby
Phone: 419.383.6883
Fax: 419.383.3251

webmaster@utoledo.edu

Genomics Core Lab - Introduction

 

  GCL SERVICES

SAMPLE SUBMISSIONS

GCL FORMS

GCL PRICING

GCL INSTRUMENTATION

ANALYSIS OF MICROARRAY DATA

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:

European Bioinformatics Institute - Microarray Introduction

National Center for Biotechnology Information - Microarrays
(ncbi.nlm.nih.gov/About/primer/microarrays)

National Center for Biotechnology Information - Gene Expression
(ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/gene_expression)

Suggested Sites:

 

                             

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











 

 

Last Updated: 6/26/15