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Director
John Ngai
Address
477 Life Sciences Addition #2751
Telephone
510 642-1165
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The Functional Genomics Laboratory (FGL) was established in January 2001
to enable an interdisciplinary group of Berkeley researchers to enter
the new post-genomics era and pursue gene expression studies at the genome-wide
level. FGL’s goals are:
- To identify, acquire, and develop state-of-the-art technologies that
will allow the large-scale study of expressed genomes;
- To develop and continually enhance computerized methods for effective
and efficient storage, retrieval, analysis, and manipulation of the
massive amount of experimental results generated in large-scale experiments
that examine gene expression at the genome-wide level;
- To provide Berkeley researchers with the technical support, infrastructure,
and service necessary to address the large-scale study of expressed
genomes, in a manner tailored to their individual research programs;
- To train Berkeley graduate and undergraduate researchers in the development
and application of cutting-edge post-genomics technologies;
- To foster collaborations in post-genomics research both among Berkeley
faculty and between Berkeley faculty and researchers around the world.
Research
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| Gene Chip |
World-wide consortia are rapidly generating the complete nucleotide sequences
of the genomes (entire DNA content) of a wide variety of organisms, including
a large number of eubacteria and archaebacteria, budding yeast (S. cerevisiae),
several plant species, nematodes (C. elegans), fruit flies (D. melanogaster),
fugu fish, zebrafish, mice, and humans. Concomitant with these genome
sequencing efforts, investigators are also attempting to determine which
sets of genes, out of the entire repertoire in an organism, are expressed
under what conditions, in which tissues, at what stage in development,
and in response to what internal or external cues. This latter information—the
“expressed genome” of an organism—has opened up entirely
new ways of addressing and understanding basic biological processes. The
methodology for assessing the expressed genes in an organism or cell is
based on using glass slides onto which DNAs corresponding to all of the
genes in a organism are arrayed in an addressable pattern. These DNA microarrays—also
referred to as “gene chips”—are then probed with mRNA
isolated from the cells or tissues of interest. In this way, a global
picture of which genes are expressed, and which are not, under any circumstance
can be obtained. With currently available technology, it is now possible
to monitor simultaneously the expression of all of the recognizable genes
in yeast (6,307), fruit flies (~14,200), worms (~19,200) and even vertebrate
species, including mice and humans (~35,000). The ability to perform such
analyses en masse provides the ability to characterize biological and
pathological processes at unprecedented levels of detail. At the same
time, this field is still in its infancy with regard to optimizing and
refining both the technology for producing and querying microarrays and
the computer-based methods for analyzing and extracting biological meaning
from such massive amounts of data.
Facilities
The Functional Genomics Laboratory has acquired and established
the full capabilities for carrying out DNA microarray analysis of gene
expression. These techniques allow the analysis of mRNA expression from
tens of thousands of genes at a time. To date, we have created high density
cDNA microarrays from the nematode worm, mouse and zebrafish. These microarrays
are being used as tools by campus researchers to investigate patterns
of gene expression in the nervous and immune systems, as well as during
embryonic development. In close collaboration with Professor Terry Speed’s
group (UC Berkeley Department of Statistics), the Functional Genomics
Laboratory is also developing improved methods for DNA microarray experimental
design and execution, image capture, and statistical analysis.
Research Support and Training
The Functional Genomics Laboratory provides research support services
for campus investigators using DNA microarray technologies in their research
programs. These services include hands-on training and consultation from
the unit’s Staff Research Associates and Principal Statistician;
software, computational facilities, and databases for gene expression
data analysis; prefabricated DNA microarrays; and a full complement of
robotics technologies for the fabrication of custom DNA microarrays.
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