Proposal Support

ICBR is expert and experienced in helping researchers prepare proposals by providing letters of support, budget information, project method descriptions and other information for use in proposal submission. ICBR staff can also be engaged as Co-Investigators, Key Personnel or other support staff, thereby allowing their CV with demonstrated expertise to be included in proposal submissions.The inclusion of ICBR staff and services in a proposal firmly establishes that work will be completed with professional expertise, both broadening and strengthening proposals.

A summary of particular core services can be found below. Use of these descriptions with proposals is welcome and encouraged. Potential ICBR customers are strongly encouraged to work directly with ICBR staff to get additional specific details on budget items, staff expertise, and equipment descriptions.

Bioinformatics Core

The Bioinformatics core offers bioinformatics and biostatistics consulting and data analysis services to help researchers toward an in-depth understanding of large-scale data sets…more.

The Bioinformatics core offers bioinformatics and biostatistics consulting and data analysis services to help researchers toward an in-depth understanding of large-scale data sets acquired from next generation DNA sequencing (NGS: 454, Ion Torrent, Illumina, and PacBio systems), gene expression, and mass-spectrometry analytical technologies. We collaborate with researchers in designing experiments and analyzing complex datasets by applying various data-analytical and theoretical methods, mathematical modeling and computational simulation techniques. We develop multiple comprehensive pipelines enabling large-scale data processing, including metagenomics (characterization of environmental microbial communities), transcriptome and genome annotation (project-based EST/genomic sequence assembly, annotation, and gene prediction), microarray-based data analysis (statistical and functional data analysis from major microarray platforms of various species), and other peer-reviewed NGS data analysis (e.g., RNA-Seq, DNA-Seq, and ChIP-Seq). Bioinformatics staff members have extensive experience in bioinformatics, genomics, transcriptomics, medical informatics, and translational research. Our expertise includes software and database development, big data analysis and statistics, and high-performance computing.

Contact: ICBR-Bioinformatics@ad.ufl.edu

Cytometry Core

The Cytometry core provides a variety of tools and expertise for cellular measurements. The laboratory incorporates numerous flow cytometers, from simple entry-level devices…more.

The Cytometry core provides a variety of tools and expertise for cellular measurements. The laboratory incorporates numerous flow cytometers, from simple entry-level devices (FACS Calibur or CyFlow-C6, BD Biosciences, San Jose, CA) to high-end 5-laser, 16-parameter instruments to analyze (LSR-II, BD Biosciences) or sort cells (Aria-II, BD Biosciences). In addition to flow cytometers, the laboratory offers a laser confocal scanning microscope (TCS-SP5, Leica Microsystems, Exton, PA). The microscope is well equipped with a variety of excitation lines from near UV to red and can collect 3 to 4 emission colors (depending on dye combinations), with viable cell time lapse and extensive computed parameter capabilities, including FRET, FRAP, image stitching, and 3D reconstruction. The laboratory offers two sites: a main site at the Cancer/Genetics Research Complex, and a satellite laboratory at the McKnight Brain Institute. Staff members are available for consultation in planning cytometric assays and carrying out the analytical portion of the assay, including analysis of the resulting data. Samples must be prepared for cytometry in the investigator’s laboratory, although if needed, some preparation capabilities exist at the Cancer/Genetics site. Training in analytical instrument operation for Investigator’s staff is also available.

Contact: ICBR-Cytometry@ad.ufl.edu

Electron Microscopy Core

The Electron Microscopy core provides microscopic imaging services on a fee-for-service basis. The core is equipped with a set of microscopes having imaging capability from…more.

The Electron Microscopy core provides microscopic imaging services on a fee-for-service basis. The core is equipped with a set of microscopes having imaging capability from whole tissues to macromolecules. They include FEI F20 cryoelectron microscope, FEI Spirit cryoelectron microscope, Hitachi H-7000 transmission electron microscope, Hitachi S-4000 scanning electron microscope, Zeiss Pascal LSM5 confocal laser scanning microscope, Olympus BH2 compound epifluorescence microscope with, and Meiji dissecting microscope. All the microscopes have digital cameras that capture high-resolution images. A full range of ancillary instruments for sample preparation such as high-pressure freezer, automatic tissue processor, and ultramicrotomes are also housed in the core. Our main services are transmission electron microscopy and scanning electron microscopy analyses. Imaging projects are carried out by core staff members or by individual researchers after appropriate training.

Contact: ICBR-ElectronMicroscopy@ad.ufl.edu

Gene Expression & Genotyping Core

The Gene Expression & Genotyping core provides a variety of gene expression services related to Affymetrix and Agilent array process including whole genomic wide gene expression arrays, miRNA array, DNA…more.

The Gene Expression & Genotyping core provides a variety of services related to Affymetrix and Agilent array process, including whole genomic-wide gene expression arrays, miRNA arrays, DNA arrays, and Gene Regulation Analysis arrays. GE also offers RNA-Seq, SAGE, small RNA and Sequence Capture libraries construction, and cDNA normalization service for different NextGen Platforms. In addition, DNA and RNA quality assessment services are offered using an Agilent Bioanalyzer.

The core also provides a variety of basic molecular biology services such as DNA isolations, PCR reactions, and PCR purifications for sequencing. We also set up most types of fragments for analysis on the AB3730xl automated sequencer; providing the buffers and size standards. The AdvanCE FS96 is a 96 capillary instrument used to analyze fragments with greater than trinucleotide repeats. In addition, the Genotyping core designs, characterizes, and processes microsatellite loci used for individual identification, population studies, and geneflow. The core has an Illumina BeadArray Reader used to analyze SNP and gene expression samples in a high-throughput fashion.

We also provide real-time PCR services by utilizing Applied Biosystems (ABI) 7500 FAST, ABI 7900HT, and BioRad CFX96. We support both SybrGreen and TaqMan reaction chemistries. Our 7900HT system is equipped with both 96- and 384-well blocks to facilitate high-throughput analysis. Applications include quantitative gene expression analysis, pathogen detection/quantification, and allelic discrimination (SNP detection). Our walk-up self service on the AB 7500 FAST allows researchers to set-up and run their own plates, but not purchase their own machine. The QUANTSTUDIO 3d DPCR SYSTEM allows customer to do absolute quantification, rare allele detection, quantification using TaqMan SNP array, and CNV (Copy Number Variation) in a more sensitive, specific, and precise way.

Contact: ICBR-GeneExpression@ad.ufl.edu

Monoclonal Antibody Core

The primary service of the Monoclonal Antibody core is the development of new mouse monoclonal antibodies. All phases of antibody development are carried out by this laboratory…more.

The primary service of the Monoclonal Antibody core is the development of new mouse monoclonal antibodies. All phases of antibody development are carried out by this laboratory: immunization of mice, fusions, screening (ELISA and western blotting), single cell cloning, mycoplasma testing and isotype determination. Other services include high density in vitro antibody production, purification and labeling of monoclonal antibodies. Assistance is also available for developing immunoassays and for determining antigen:antibody binding constants using the Octet QKe from ForteBio (BioLayer Interferometry).

Contact: ICBR-MonoclonalAntibody@ad.ufl.edu

NextGen DNA Sequencing Core

The NextGen DNA Sequencing core at the Interdisciplinary Center for Biotechnology Research (ICBR) provides researchers with quality, massively parallel, high-throughput sequencing data…more.

The NextGen DNA Sequencing core at the Interdisciplinary Center for Biotechnology Research (ICBR) provides researchers with quality, massively parallel, high-throughput sequencing data using the most current instrumentation, at a reasonable cost. We currently support the most popular platforms: LifeTech (Fisher Scientific) Ion Torrent PGM and Ion Proton systems, Illumina NextSeq500 and MiSeq (as well as HiSeq through third-party providers), and the Pacific Biosciences SMRT system. Together, these instruments cover a broad range of powerful applications, thus allowing biologists to investigate and obtain answers to questions that were not attainable until recently. Our free consultation services aim to help researchers navigate through the complex matrix of experimental options represented by the available sequencing technologies. Some of these important considerations include: read length, error rate, predominant type of error, data output/run, speed, cost, etc. The ever-broadening range of applications include (but are not limited to) de novo sequencing of whole genomes, targeted sequencing, transcriptome sequencing (RNA-seq), chromatin immunoprecipitation (ChIP) sequencing, methylation analysis, and metagenomics.

Contact: ICBR-NextGenSeq@ad.ufl.edu

Proteomics & Mass Spectrometry Core

The Proteomics & Mass Spectrometry core provides a variety of services related to protein fractionation, qualitative and quantitative mass spectrometry analysis, de novo protein sequencing and…more.

The Proteomics & Mass Spectrometry core provides a variety of services related to protein fractionation, qualitative and quantitative mass spectrometry analysis, de novo protein sequencing and protein database searching. Protein sequencing and identification are routine procedures in the lab. The capabilities in quantitative proteomics include iTRAQ® (Isobaric Tags for Relative and Absolute Quantitation), cysTMT (Tandem Mass Tags), SILAC (Stable Isotope Labeling of Amino acids in Cell cultures), and a MRM (Multiple Reaction Monitoring) based absolute protein quantification. Along with our capacities of separating thousands of proteins and characterizing differential protein expression, we have a suite of state-of-the-art mass spectrometers available for biomedical and advanced technology research, including a MALDI-TOF (Matrix Assisted Laser Desorption Ionization- Time-of-Flight), a MALDI-TOF/TOF (4700 Proteomics Analyzer, AB), two quadrupole time-of-flight instruments (QSTAR XL and QSTAR Elite, AB), a quadrupole-linear ion-trap (4000 QTRAP, AB), and an advanced LTQ Orbitrap system. These instruments are mainly used for accurate molecular weight determination, protein identification, posttranslational modification, expression analysis (using in vitro isotope labeling, SILAC in vivo labeling, and label free). Our facility is also set up to provide Edman de novo N-terminal protein sequencing, and sample fractionation using HPLC. To ensure success and maximize productivity, the facility offers education, consultation, data processing and reporting, and support of grant application.

The core also provides a variety of services related to Biomarker Discovery, such as protein abundance analysis using gel-based 2 -D Fluorescence Difference Gel Electrophoresis (2-D DIGE); protein separation using 1-D or regular 2-D gel electrophoresis and Western blotting; 2-D gel-based phosphor protein and glycoprotein profiling. For these services we have instruments such as Ettan IPGphor, Ettan DaltSix, Typhoon Trio+ phosphor scanner, Investigator ProPic automatic spot picker. In addition, we have image analysis softwares such as GE’s DeCyder and Non-Linear Dynamics SameSpot Progenesis with Stats. Furthermore, the core provides protein enrichment and abundant protein depletion from biological fluids such as plasma, CSF, and urine using different techniques such as combinatory peptide (ligand) library, and assorted immunodepletion. We also provide liquid phase preparative IEF to fractionate protein or peptide mixture using an Agilent 3100 Offgel fractionator. Moreover, the core provides training on using Surface Plasmon Resonance (SPR) technology to study molecular interaction. We have Biacore 3000 for therapeutic drug discovery, antibody screening, and ligand fishing, and other applications including affinity measurements, binding kinetics, binding specificity, epitope mapping, and active concentration assay.

Contact: ICBR-Proteomics@ad.ufl.edu

Sanger Sequencing Core

The Sanger Sequencing core of the Interdisciplinary Center for Biotechnology Research (ICBR) at the University of Florida has the instrumentation, expertise, and trained and…more.

The Sanger Sequencing core of the Interdisciplinary Center for Biotechnology Research (ICBR) at the University of Florida has the instrumentation, expertise, and trained and dedicated staff to help you with low, medium, and high throughput Sanger DNA sequencing services. We are currently using a standard Sanger sequencing method on several platforms (e.g., Applied Biosystems 3730xl and AB 3130 DNA Analyzers).

In terms of data management, the Sanger Sequencing laboratory projects are tracked by the dNAtools laboratory information management system. This LIMS manages all aspects of the DNA sequence production process including: generating sample sheets, tracking pending and completed sequencing jobs, and compressing, storing and archiving all DNA sequence data. You will be provided with a secure password-protected project directory for your DNA sequence data. Of course, assistance with compilation and analysis of Sanger sequence data is available from the Bioinformatics division of the UF ICBR.

Contact: ICBR-SangerSeq@ad.ufl.edu