The satellite facility at OSU consists of two interoperating units, the
OSU Microarray Core Facility and BioinfOSU. The OMCF has modern
microarray printing, scanning and data analysis capabilities and
provides consultation and training in the form of workshops in
microarray analysis. BioinfOSU supplies the OMCF with software for the
analysis of microarray data, particularly the popular Gene Pix
Autoprocessor (GPAP), a web-based application providing preprocessing
of raw microarray data. GPAP performs signal filtering, background
correction and signal normalization and provides diagnostic plots and
reports to evaluate data quality and the effects of preprocessing.
GPAP can also identify the top differentially expressed genes for the
user. In addition to supplying the supporting computer infrastructure
for the OMCF efforts, BioinfOSU provides other bioinformatics resources
to scientists. It hosts the PipeOnline tool for processing and
annotation of ESTs and VirOligo, a database of oligonucleotides used
in virus detection. A variety of software packages are provided for
The University of Oklahoma Bioinformatics Core Facility hosts a fully functionial,
web-accessible microarray database, developed with funding from the NSF-EPSCoR and NIH-BRIN.
The OU Microarray Database (OUMDB) provides users of the Oklahoma Bioinformatics
Network a web interface to upload, manage, and analyze microarray experiments.
The OU Microarray Core Facility provides equipment for microarray printing, hybridization and
scanning. The staff of the OU Bioinformatics Core includes skilled programmers who regularly
tailor the database to accommodate user needs. Specifically, the OUMDB provides password-protected
access to features including a complete LIMS, array-design, data-upload interface, statistical package,
experiment organization, and data-mining package. The OU E. coli Gene Expression Database hosted by
OUMDB offers the most extensive publicly accessible E. coli microarray datasets in the world.
The Laboratory for Genomics and Bioinformatics is a genomics facility offering DNA sequencing
(custom and genome-scale projects), genotyping, microarray design, hybridization and data analysis,
and other services. Custom microarrays have been designed for several bacterial genomes, including
Actinobacillus actinomycetemcomitans, Haemophilus ducreyi, Neisseria gonorrhoeae, Staphylococcus aureus,
and Streptococcus pyogenes. The OUHSC core facility offers microarray hybridization and data analysis
services, and data archival using the open source BASE database format. A free Perl workshop is periodically
offered on the OUHSC campus to introduce interested individuals to the language and its use in bioinformatics.
Among the programming languages available, Perl is arguably the favorite of bioinformatics programmers.
Its low learning curve and flexible syntax make it an ideal beginning language for biologists, and its
unsurpassed text-parsing ability make it an excellent choice for data such as protein and nucleic acid
sequences. This informal, non-accredited workshop consists of four two-hour sessions spanning two weeks.
You will not walk away from these sessions a Perl expert, but you should have a working knowledge of the
basic syntax of the language and programming structure that will help you carry on further self-study.
No previous programming experience is required. The only prerequisites are an understanding of operating
system usage in windows or linux, such as creating files and folders and using a text editor. Very general
knowledge of biological processes such as transcription and translation also will be assumed. Class sizes
will be small and students will follow the instructor on laptop computers provided by the workshop.
Scientists at the OMRF Microarray Research Facility collaborate with researchers
at OMRF and around the world to study differential gene expression in order to understand
pathophysiologic states at the molecular levels. They manufacture human, mouse, and
Candida albicans oligonucleotide microarrays, plus a variety of custom cDNA
microarrays containing genes from libraries produced by individual investigators.
Links to gene lists on oligonucleotide arrays are available to download to your computer.
A variety of protocols, available online, have been developed and optimized at OMRF to
assist investigators here and elsewhere in the use of microarrays. The Microarray Facility
Bioinformatics Section designs novel analytical tools for use in microarray studies, and
assists users in analyzing and understanding microarray data obtained from experiments performed
at the Facility. Links to recent publications and public databases available for downloading
to your computer are also listed.
The Department of Biological Science at the University of Tulsa recently purchased the Affymetrix
GeneChip® platform for the measurement of mRNA expression. The system includes the GeneArray®
Scanner, the Fluidics Station 400, the Hybridization Oven 640, and a powerful computer
workstation. GeneChip® expression arrays are available for the study of human, rat, mouse,
drosophila, C. elegans, E. coli, and many other model systems. The services available from the
TU Microarray Core include Northern blot for mRNA quality control, clean-up of total RNA,
target labeling, hybridization, scanning, and biostatistical analysis of the data.