Overview
Divisions » Bioinformatics | Cellomics | Genomics | Proteomics
Gene-based analysis remains at the forefront of life-sciences discovery. In our role as a research support organization, the Genomics Division of the ICBR has one singular mission: Provide the means for specialized genetic data acquisition, and at reasonable cost. Our group philosophy is that scientists should not be burdened with creating and maintaining the technical infrastructure to generate, store, and analyze genomic data, but instead focus on using this information for scholarly publication and for developing external funding opportunities. The Genomics Division provides life scientists on campus and in other state institutions with services that include large- and small-scale DNA sequencing, genetic analysis, gene expression using microarrays, SNP genotyping and quantitative or real-time PCR.
The Sanger Sequencing (Savita Shanker, PhD) group uses state-of-the-art capillary array sequencers, ABI 3130 (up to 16 capillaries), 3730xl (96-capillary) and the 384-capillary MegaBACE 4500 sequencer, to sequence DNA from purified templates or bacterial cultures.
The 454 Sequencing (Regina Shaw) group has a design capacity of over 600 million bases of high quality sequence per month due to a newly acquired 454 Life Sciences DNA sequencing unit, GS20, which is capable of generating an average of 30 million bases of sequence in a 4-hour run. A broad spectrum of projects utilizing the pyrosequencing technology in GS20 instrument included, among others, sequences of four bacterial genomes, multiple individual chloroplast genomes, several metagenomics surveys of environmental samples, transcriptome profiling using normalized and non-normalized cDNA libraries, and transposon-insertion site profiling technology.
The Genetic Analysis (Ginger Clark, MS) group applies molecular technology to studies in ecology, evolution, and conservation biology. The staff develops projects from sampling strategy through final publication, and provides extensive support in the analysis and interpretation of DNA sequence data. Mitochondrial DNA sequences are the primary methodology used for population and evolutionary studies. Second generation fingerprinting assays (using microsatellite libraries) are used for fine scale analysis of populations and for pedigree determinations.
Our Gene Expression (Gigi Ostrow, PhD) group can assist a client develop a statistically valid experimental design. Services most often include complete Affymetrix and Agilent sample preparation and labeling from total RNA samples. In many cases where the client prefers to do their own chemistry, we provide array hybridization and array scanning services. Although microarrays have the ability to simultaneously evaluate the expression level of thousands of gene transcripts, they are not extremely quantitative.
Our Real-time PCR (Li Zhang, PhD) (RT-PCR) group can assist users to obtain precise, quantitative information (hence, the name qPCR) on gene expression of smaller number of gene species. The ABI Prism 7900HT is designed for performing RT-PCR in either 384-well microplate format or in credit-card size micro card format. The latter can be customized to assay from 1 to 384 genes using only a two-microliter sample volume.
A high-throughput technology platform by Illumina that supports a range of life science applications including SNP genotyping (David Moraga, PhD) and RNA profiling done in a massively parallel fashion will be available in Spring 2007.
Direct Genomics Division Inquiries to Ernie Almira, PhD…