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 clients are strongly encouraged to work directly with ICBR staff to get additional specific details on budget items, staff expertise, and equipment descriptions.
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 sequencing (NGS: 454, SOLiD, Ion Torrent, Illumina GAII, 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 have developed multiple comprehensive pipelines that enables researchers to process large-scale data, including metagenomics (characterization of microbial communities found in harsh Arctic climates, termite guts, and premature infants), 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).
Electron Microscopy and Bioimaging Core
The Electron Microscopy and Bioimaging 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 and Bioimaging 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.
Flow Cytometry Core
The Flow 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 Flow 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
, 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.
Gene Expression Core
The Gene Expression core provides a variety of services related to Affymetrix and Agilent array process including whole genomic wide gene expression arrays, miRNA array, DNA…more.
The Gene Expression core provides a variety of services related to Affymetrix and Agilent array process including whole genomic wide gene expression arrays, miRNA array, DNA arrays, Gene Regulation Analysis arrays. GE also offers RNA-Seq, SAGE, small RNA and Sequence Capture libraries construction for different NextGen Platform. GE also has Agilent Bioanalyzer used to do quality assessment for DNA and RNA samples. In addition, we also provide cDNA normalization service for NextGen application.
The Genotyping core provides a variety of basic molecular biology services such as DNA isolations, PCR reactions, and PCR purifications for sequencing…more.
The IGenotyping core 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 standard. 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.
The primary service of the Hybridoma core is the development of new mouse monoclonal antibodies. All phases of hybridoma development are carried out by this laboratory…more.
The primary service of the Hybridoma core is the development of new mouse monoclonal antibodies. All phases of hybridoma 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).
Mass Spectrometry Core
The 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 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.
NextGen DNA Sequencing Core
The NextGen DNA Sequencing core belongs to the Genomics Division of the Interdisciplinary Center for Biotechnology Research (ICBR). Its services include a wide array of applications…more.
The NextGen DNA Sequencing core belongs to the Genomics Division of the Interdisciplinary Center for Biotechnology Research (ICBR). Its services include a wide array of applications using cutting-edge next generation DNA sequencing technologies such as Roche’s 454 GS-FLX with XL-plus upgrade, LifeTech’s SOLiD 5500xl and Ion Torrent PGM systems, Illumina’s Genome Analyzer, and Pacific Biosciences’ SMRT system. The ever-broadening range of applications includes de novo sequencing of whole genomes, targeted sequencing, transcriptome sequencing (RNA-seq), chromatin immunoprecipitation (ChIP) sequencing, methylation experiments, and metagenomics. The facility’s personnel provide free consultation on cost considerations, plate configurations, and platform-specific applications.
Protein Biomarkers Core
The Protein Biomarkers core provides a variety of services related to Biomarker Discovery, such as protein abundance analysis using gel-based 2 -D Fluorescence Difference Gel…more.
The Protein Biomarkers core 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.
Quantitative PCR Core
ICBR provides two different instruments to support the real-time PCR needs of the research community, the Applied Biosystems (ABI) 7500 FAST and ABI 7900HT. Both machines…more.
ICBR provides two different instruments to support the real-time PCR needs of the research community, the Applied Biosystems (ABI) 7500 FAST and ABI 7900HT. Both machines support SYBR® or TaqMan™ reagents allowing absolute, relative, relative standard or comparative Ct quantification. Applications include quantitative gene expression analysis, pathogen detection/quantification, allelic discrimination (SNP detection), and mutation screening. Flexibility for different budgets and technical skill levels is provided by offering two different types of service; walk-up self service on the AB 7500 FAST for researchers that want to set-up and run their own plates but not purchase their own machine, and technician assisted service on the AB 7900HT that supports 96 and 384 well formats, 384 TaqMan Array and FAST 96 well.
Sanger Sequencing Core
The Sanger Sequencing core of the Interdisciplinary Center for Biotechnology Research (ICBR) solicits DNA samples from all over the United States for sequencing on fee basis. Automated…more.
The Sanger Sequencing core of the Interdisciplinary Center for Biotechnology Research (ICBR) solicits DNA samples from all over the United States for sequencing on fee basis. Automated DNA sequencing is performed using ABI big dye chemistry and ABI 3730xl and 3130xl genetic analyzers. The services include standard DNA sequencing on user provided purified single or double stranded plasmid DNA or PCR products, sequencing on large size clones, 96-well sequencing on bacterial cultures and PCR products, and load only DNA sequencing. The primer walking and sequence alignments for inserts greater than 2kb are also available. We also offer technical advice on the best strategy for individual sequencing project and troubleshooting of sequencing reactions.