The PBRC Genomics Core Facility (GCF) offers the Applied Biosystems
1700 array system and Illumina system for human, mouse, and rat whole
genomes. The systems are housed in a fully equipped, secure laboratory.
The GCF offers sample
quality control, labeling, hybridization, scanning, quantitation, and
data analysis services.
Please note that Applied Biosystems has chosen
to discontinue manufacture of their array system in December 2008.
The GCF will support this platform until that date.
Additionally, the microarray facility produces high-density custom
microarrays from researcher provided cDNA or oligonucleotide libraries.
Slides are printed with a GeneMachine OmniGrid Microarrayer equipped with
server arm and scanned using a Perkin-Elmer ScanArray 5000.
Normalization and analysis (fold-change, log2 fold-change, p-value,
false discovery rate (BH), and fold-change bins) are provided for
Applied Biosystems 1700 data sets. Guidance and support of the investigator
are provided as he or she utilizes the software tools available for more
in-depth analysis. Most frequently used software packages include
R-Script
for normalization and basic analysis,
Panther,
for gene annotation, biological pathways, molecular functions and
protein families, and Spotfire for pattern visualization.
Gene validation is supported through access to Applied Biosystems 7900HT Sequence
Detection Systems for quantitative
real-time PCR.
For help in designing a microarray experiment, please
contact us.
It is necessary for individuals who are considering running microarrays in
our facility to discuss technical and statistical aspects of the design of
their experiments before the experiment is performed, i.e. before RNA is isolated.
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