Overview of the Microarray Component of the ParaBioSys PGA
The Microarray Core component of the ParaBioSys PGA has been responsible
for the development of oligonucleotide probe sets for DNA microarray
production. Because of the high cost associated with commercial probe
sets and instrumentation needed for microarray fabrication, the Microarray
Core was established to design, synthesize, and produce oligonucleotide
probe sets and printed microarrays for the NHLBI academic community.
Our goal is to make microarray technology and experimentation more
accessible to the inexperienced laboratory by offering cost-effective
microarray reagents and services, as well as educational programs in
general microarray methodology and data analysis.
The following schematic depicts an overview of the processes that the
Microarray Core employs for oligonucleotide probe design and synthesis,
quality control, and array fabrication. Oligonucleotide probes are
designed using the OligoPicker software package developed by the
Bioinformatics component of ParaBioSys. Using this versatile software,
70mer oligonucleotide probe sets have been designed for the mouse,
human, rat, cow, chicken and pig genomes. The probes are synthesized
using standard phospohoramidite methods and are modified at the
5'-terminus to facilitate covalent coupling of a probe to the microarray
surface. Each probe is quantified and analyzed by either capillary
electrophoresis or mass spectroscopy to ensure that the probe is of the
desired length and purity. After quality control analysis, probe sets
are made available to the academic community for cost of production.
The Microarray Core also produces pre-printed slides that have undergone
extensive quality control testing to assess printing performance during
production.
For a detailed presentation of processes involved in the production of
probe sets and microarrays, please select the topic of interest from
the scheme below.
Microarray Products of the ParaBioSys PGA
Pre-printed microarrays currently available
Microarray Oligonucleotide sets
Public Microarray Data
Bioinformatic Resources
Tutorials in Microarray Data Analysis
Massively Parallel Real Time PCR
We have developed an experimentally validated algorithm for the
identification of transcript-specific PCR primers on a genomic scale. Our
online database, PrimerBank,
has been created for researchers to retrieve
primer information for their genes of interest. PrimerBank currently
contains 177,516 primers encompassing most known human and mouse genes. The
primer design algorithm has been tested by conventional and real-time PCR
for a subset of 1,184 primers with a success rate of 99%. We are now
building on these preliminary data to generate a comprehensive collection of
experimentally validated primers. Such a collection will enhance the
abilities of scientists to explore precise changes in expression of their
genes of interest, and will allow the initiation of global transcript
abundance monitoring by massively parallel PCR methods.
|