University of Florida | ICBR

Instrumentation at a Glance

LSR-II, Aria Cell Sorter, 454 Genome Sequencer 20, BLAST, BlastQuest, Custom Sequencing, Genotyping, Illumina BeadStation 550GX, Protein Sequencing, SNP Genotyping, …

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Bioinformatics

Bioinformatics Instrumentation

Paracel Blastmachine2: Commercial Blast search platform with twenty-eight 2.4 GHz processors
Mascot Server: In-house built server with 16G RAM and eight 2.4GHz processors
Linux Farm: Runs database and web server applications, Glimmer2, Paracel TranscriptAssembler, FGENESB, BlastQuest, phred, phrap, and consed.
Paracel TranscriptAssembler (Paracel Inc., Pasadena, CA): Highly optimized commercial software package specifically designed for assembly and analysis of large-scale EST sequencing projects.
Geospiza Finch Suite (Geospiza, Inc., Seattle, WA): DNA sequence management and DNA sequence data server system. Manages DNA sequencing queue, tracks project and user data.
Phred, Phrap, Consed (Genome Center, University of Washington, Seattle, WA): Comprehensive base calling, contig assembly, and sequence editor for large-scale DNA sequencing and assembly projects. The de facto standard for DNA sequencing used by all major genomics laboratories.
BlastQuest Blast Results Manager: In-house developed web-based data server for warehousing homology search results required throughout large-scale DNA sequencing projects. Parses XML-based BLAST results files into MySQL database for selective search, summary, and data filtering.
BLAST: Maintain local copies of NCBI sequence databases and BLAST executables. Command line control of BLAST homology searches for all large-scale DNA sequencing projects.
FGENESB (Softberry Inc., Mount Kisco, NY): Operon and gene finding package for bacteria.
Special Purpose Custom Software: We maintain a wide variety of special purpose software for microarray data and DNA sequence analysis.

Cellomics Instrumentation

Electron Microscopy & Bioimaging (Byung-Ho Kang)

Hitachi H-7000 TEM

Installed 1991
Maximum Resolution: 0.2nm
Magnification: 110x-600,000x
Accelerating Voltage: 25-125kv
Soft-Imaging System MegaView III with AnalySIS
Output: EM4489 film,Tiff on CD-ROM/DVD/FTP

Hitachi S-4000 FE-SEM

Installed 1990
Maximum Resolution: 1.5nm
Magnification: 18x-300,000x
Accelerating Voltage: 0.5-30kv
Advanced Database Systems Digital Capture Card
Output: 120mm Roll Film, Type 55 Polaroid, Tiff on CD-ROM/DVD/FTP

Olympus BH-2 Epifluorescent Microscope

Installed 1998
Objectives: 4x, 10x, 20x, 40x, 100x oil
Phase Contrast
Pixera 120C Digital Camera
Fluorescent Filter Arrays:
- Chroma Technology #31013 DAPI/Hoechst/AMCA/Cascade Blue
- Chroma Technology #41001 FITC/RSGFP/Bodipy/Flou 3/DiO
- Chroma Technology #51004 Dual Band FITC/TRITC or Cy2/Cy3
- Chroma Technology #51007 Dual Band Cy3/Cy5

Ultramicrotomes

Leica Ultracut E
Leica Ultracut R
Reichert Supernova
Microm HM 505E Cryostat

Cryostat HM 505E

Bal-Tec 030 Critical Point Dryer

Zeiss Pascal LSM5 Confocal Laser Scanning Microscope

Installed 2005
Axiovert 200 microscope with 10X, 20X, and 40X objective lenses
Argon-laser (458/488/514 nm)
Helium-neon laser (543 nm)
Helium-neon laser (633 nm)
Differential intereference contrast and epifluorescence microscopy capability with digital imaging

Flow Cytometry (Neal Benson,MS)

LSR-II: The LSR-II incorporates 3 lasers (violet, blue, and red) for excitation. It has a flexible detection system that can simultaneously acquire emission data from up to 11 fluorochromes, in addition to forward and side light scatter.
Aria Cell Sorter: The FACS Aria cell sorter incorporates 4 lasers (UV, violet, blue and red) and can simultaneously detect up to 14 fluorochromes in addition to forward and side light scatter. It offers high speed cell sorting (5-15,000 cells per second) of up to 4 subpopulations into tubes, or it can deposit specific numbers of separated cells in a matrix pattern on a microscope slide or into wells of a microtiter plate.
FACScan: This is the most basic instrument we have. It can analyze forward and side light scatter, and up to 3 colors (green, orange, and red) of fluorescence. It has a single laser that emits 488 nm (blue) light.
FACSort: This is similar to the FACScan. In addition to the above analysis functions, it adds low speed (<300 cells/second) cell sorting capability. Since cells are totally contained during the sort process, it is often used for sorting small numbers of cells under BSL-2 conditions.
FACSCalibur: Similar to the FACScan, but it adds a 2nd laser that emits 635 nm (red) light and a 4th fluorescence detector, so it can analyze more fluorescent dyes simultaneously. We have 2 FACS Calibur instruments; one is equipped with an automatic sample tube changer.
CyAn: Contains 3 lasers (blue, red, and violet) and can measure forward and side scatter, and up to 9 colors of fluorescence. The CyAn is appropriate for work utilizing more than 4 fluorochromes, or work involving fluorochromes that, due to their uncommon spectral characteristics, can not be analyzed on the other instruments.
FACS Vantage SE Turbosort: Contains blue and red lasers, as well as a krypton laser that is tunable to either violet (413 or 407) or ultra-violet. It can measure forward and side scatter, and up to 8 colors of fluorescence. The major function of this instrument is sorting, or separating, cell populations at high-speed (10,000 cells/second or more). The DiVa option adds digital signal processing electronics, improving overall speed and purity of the sorted populations, and allowing sorting of 4 subpopulations at once or distribution of a single subpopulation in the wells of microtiter plates.

Hybridoma (Linda Green)

Cell Culture:

Biosafety hoods
CO2 incubators
Inverted phase contrast microscopes
Refrigerated centrifuges
-85 degree ultralow freezers
Self filling liquid nitrogen freezers
Programmable freezing machine (Cryomed)

Freezes cells at a controlled rate

Analytical

Microplate washers
Microplate readers from Molecular Devices (multimode, tunable to any wavelength: absorbance, luminescence, fluorescence)
Gel electrophoresis
Minigel systems (Invitrogen), Phastgel system (GE Healthcare) semi-automated small scale rapid electrophoresis system.

Genomics Instrumentation

454 Sequencing (Regina Shaw)

Genome Sequencer 20™ System:: A a complete system solution for ultra-high throughput DNA sequencing. The system consists of the Genome Sequencer 20 instrument, software, reagents, consumables and accessories. The reagents provide a start to finish solution from library construction to amplification and sequencing. The included software enables mapping and de novo assembly of genomes up to 50 megabases.

Gene Expression (Gigi Ostrow, PhD)

Affymetrix GeneChip® system: This includes an Affymetrix 450 fluidics station, 3000 scanner, hybridization oven and GeneChip operating software.
Agilent 2100 Bioanalyzer for DNA and RNA analysis
Agilent 2-dye scanner that is compatible with any 1' x 3' glass slide.: Feature extraction software includes Agilent Feature extraction 9.1 and Imagene. Data analysis software includes Rosetta's Luminator software, JMP Genomics, BRB array tools and several others.

Genetic Analysis (Ginger Clark, MS)

Amersham MegaBACE 1000 96 capillary sequencer Eight Biometra thermocyclers

Realtime PCR (Li Zhang, PhD)

Applied Biosystems 7900HT Fast Real-Time PCR Systems: The Applied Biosystems 7900HT Fast Real-Time PCR System is the only real-time quantitative PCR system that combines 96- and 384-well plate compatibility and the TaqMan® Low Density Array with optional fast real-time PCR capability to facilitate high throughput analysis. The instrument is capable of real-time, end point and dissociation curve analysis. Relative Quantitation Software allows gene expression data from up to ten plates to be combined in one analysis.
Applied Biosystems 7500 fast Real-Time PCR system: The Applied Biosystem 7500 Real-Time PCR System is a leading edge system with features to support labs requiring more capabilities from their real time PCR platform. The 7500 Fast Real-Time PCR System Enables standard 96-well-format high-speed thermal cycling delivers results in less than 40 minutes!
Applied Biosystems 7700 Sequence Detection System: The instrument is capable of real-time, end point and dissociation curve analysis of assays arrayed on multiple formats. 7700 sequence detection system combines 96 well plate and PCR tube compatibility.

Sanger Sequencing (Savita Shanker, PhD)

The following are our sequence related instrumentation:

One ABI 3730-96 capillary sequencer, and two ABI3130-16 capillary sequencers interfaced with Dell computers for controlling sequencer functions and managing files.
One Amersham Pharmacia Biotech MegaBACE 1000 capillary array DNA sequencer and one MegaBACE 4500 capillary sequencer.
Two Robbin Scientific Hydra-96 equipped with 96 100ul capacity syringes and Duraflex needles and two MATRIX Hydra II . Preparation and post reaction processing of cycle sequencing reactions in 96-well and 384-well formats.
One Genetix colony picker.

SNP Genotyping (David Moraga, PhD)

Illumina BeadStation 500GX: We perform high-throughput genotying using the Illumina BeadStation 500GX. This powerful genotyping system includes a high resolution (0.8 microns) laser scanner (BeadScanner) and the BeadStudio software for low-to-high throughput SNP analysis.

Proteomics Instrumentation

2-D Difference Gel Electrophoresis (Marjorie Chow, MS)

Ettan IPGphor 3 Ettan DALT 6 vertical SDS PAGE Typhoon 9400 and 8600 variable mode imager (GE Healthcare) Decyder 6.5, Progenesis SameSpot and PG220 gel image analysis software Investigator™ Proteomic System featuring ProPic, ProGest, and ProMS (Genomic Solutions)

Peptide Synthesis (Alfred Chung, MS)

CEM Discover Microwave-assisted peptide synthesizer Advanced ChemTech Apex 396 ABI 430, 432, and 433 peptide synthesizers

Mass Spectrometry and Protein Characterization (Scott McClung)

Hybrid quadrupole-TOF (ABI QSTAR XL) equipped with LC Packings Ultimate HPLC system Hybrid quadrupole-linear ion trap (ABI 4000 QTRAP) equipped with Tempo nanoHPLC system Ion trap (Thermo LCQ Deca) MALDI-TOF/TOF (ABI 4700 Proteomics Analyzer)

Protein Characterization (Scott McClung)

494HT Procise (ABI) protein sequencer 420H Derivatizer (ABI) amino acid analyzer Biacore 3000 (contact Marjorie Chow, MS) Agilent 1100 HPLC system

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