The Bioinformatics Core offers support for the preparation of grant proposals that involve a computational / data analysis component.  We can help generate preliminary data, develop analysis strategies, identify software and hardware requirements and write the relevant proposal sections. We also provide the appropriate Resources and Equipment pages.  This service is free provided that, in case the grant is funded, the related work will be performed by our core.

Please note that although BI core members cannot receive salary support from grants, they can be included in proposals as named investigators, and can provide biosketches documenting their expertise.

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.

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 electron microscope, Hitachi H-7000 transmission electron microscope, Hitachi SU5000 scanning electron microscope, Zeiss Pascal LSM800 confocal laser scanning microscope. 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.

Please provide:

• Proposal Title
• Granting Agency
• Section of Grant
• Deadline

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.

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).

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: Illumina NextSeq500 and MiSeq, HiSeq3000 and the Pacific Biosciences SEQUEL 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.

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), TMT (Tandem Mass Tags), SILAC (Stable Isotope Labeling of Amino acids in Cell cultures), and MRM (Multiple Reaction Monitoring)-based absolute protein and metabolite 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/TOF (4700 Proteomics Analyzer, AB), a quadrupole time-of-flight instrument (QSTAR Elite, AB), a quadrupole-linear ion-trap (4000 QTRAP, AB), a LTQ XL Orbitrap system, a Q-Exactive Plus Orbitrap, a TSQ Altis, and an Orbitrap Fusion (Thermo Scientific). These instruments are mainly used for accurate molecular weight determination, protein identification, post-translational modification, expression analysis (using in vitro isotope labeling (iTRAQ and TMT), SILAC in vivo labeling, and label free). Our facility is also set up to provide mass spectrometry-based N-terminal protein sequencing, sample preparation, and 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 phosphoprotein and glycoprotein profiling; Luminex biomarker discovery. For these services, we have instruments such as Ettan IPGphor, Ettan DaltSix, Typhoon Trio+ phosphor scanner, Investigator ProPic automatic spot picker, and FlexMap3D. In addition, we have image analysis software, such as GE 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 (ProteoMiner), and assorted immunodepletion. The core also provides liquid phase preparative IEF to fractionate protein or peptide mixture using an Agilent 3100 Offgel fractionator.