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 Next Generation, or NextGen Sequencing group (nextgenseq@biotech.ufl.edu) offers cutting-edge DNA sequencing services on the Roche 454 Genome Sequencer (GS) FLXTM Standard, FLX TitaniumTM and Applied Biosystems (AB) SOLiDTM instruments. NextGen technologies make possible sequencing projects that may have previously not been feasible due to cost or technical constraints.
The Roche 454 GS-FLX is the only NextGen sequencing technology available to date that can provide long read lengths (about 250 for the FLX standard and about 300-400 bases for the FLX Titanium series). This pyrosequencing-based platform can be utilized in a variety of projects including de novo sequencing supported by shotgun and paired-end applications, comparative genomics using whole genome sequencing, amplicon resequencing, metagenomics and transcriptome analysis, gene regulation studies and ChIP sequencing.
The AB SOLiD sequencing platform is a short-read DNA sequencing-by-ligation technology that can produce more than 4 gigabases of data in a single slide run. High-quality 35-bp reads are generated by a two-base interrogation of DNA templates during sequencing. Applications using the fragment and mate-pair libraries include rapid resequencing of genomes, amplicon sequencing for large SNP detection projects or ultra deep sequencing to detect rare mutations in complex samples, metagenomic analysis, transcriptome analysis, small and micro RNA analysis, ChIP SEQ experiments and methylation studies.
Any further questions about these sequencing services should be directed to nextgenseq@biotech.ufl.edu.
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; Yanping Zhang, 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.
Real-time PCR (Sharon Norton, MS ) services offered by ICBR, including the Applied Biosystems (ABI) 7900 HT and ABI 7500 FAST real-time PCR machines, provide a unique opportunity for researchers to customize applications to fit their level of technical involvement and budgets from quantification to customizable 384 well microfluidic card arrays.
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.
Bacterial Genome Finishing Program (Dibyendu Kumar, PhD) In keeping with the ICBR goal to provide world-class research support to the University of Florida research community, its sequencing program now includes publication-quality finishing and detailed analysis of the genome of different representatives of microbial world. ICBR Genomics Bacterial Genome Finishing Program helps transform draft microbial genome assemblies into finished versions where all repeats regions are identified correctly, gaps are closed, and all bases are correctly positioned with high confidence.
Our finishing pipeline encompasses all phases of a complete sequencing effort, from library construction through genome assembly and annotation. The finishing process includes activities of bioinformatics as well as wet-lab experiments. Sequence data is finally inspected for quality, discrepancies, coverage and contiguity error rate of less than one in 10,000 bases.
Direct Genomics Division Inquiries to Ernie Almira, PhD…