Description of the Research Resources Center at UIC

This review of our organization and services is provided for investigators who need information about the RRC for inclusion in their grant applications. Please feel free to include all or any portion of these documents into your grant as your needs require. See also the Short Description of this review.

Overview

The Research Resources Center (RRC) of the University of Illinois at Chicago (UIC) is a division of the Office of the Vice Chancellor for Research. The RRC has been providing core support for research at UIC for over 50 years. RRC personnel provide user access to instrumentation, training on use of the instruments, and their own service and expertise in the application of resources for the purpose of solving of a wide range of problems for chemical, biological and structural characterization. At present its research support services consist of 20 cores, centers and laboratories: The Imaging Center (light microscopy); Electron Microscopy; MRI and Animal Imaging; Research Histology and Tissue Imaging; Flow Cytometry; Mass Spectrometry, Metabolomics and Proteomics; DNA Services & Genomics; the Center for Research Informatics; the Protein Research Laboratory; the Molecular Interactions Laboratory; High Throughput Screening Laboratory; The Center for Structural Biology; the Transgenic Production Service; the Center for Cardiovascular Research core; The Nanotechnology Core Facility; Scientific Instrument Shop; and scientific Supply Center. In the past decade the RRC has expanded markedly, adding 10 new cores while consolidating and expanding others. The RRC occupies roughly 48,000 sq ft of laboratory and office space in seven locations, and it currently has over 65 employees with each shared resource directed by a PhD scientist.

An Executive Advisory Panel consisting of six faculty members along with the Associate Deans of Research from the five research intensive colleges advise the RRC with respect to the long-term needs of the faculty. In addition, smaller, three-member committees consisting of funded users of each research service advise the facility directors and the RRC administration. The UIC administration supports the RRC by providing approximately one third of the operating cost and additionally contributes to new equipment purchases. Another important source of funding is grants obtained in collaboration with campus investigators and when necessary supplemented with matching money from the UIC units. Nearly 2,000 investigators made use of RRC services in the last fiscal year. The basic (non-capital) operating budget was approximately $9 million in FY13. Over the last 5 years, $12M in new instrumentation has been added using UIC, and federal funds with two NSF MRI and six NIH S10 grants.

RESEARCH SUPPORT SERVICES

The Imaging Center is staffed by three PhD scientists and is equipped with 8 microscopes to assist in a wide variety of biological studies. Investigators can study complex cellular processes, structure and function in vivo using single cells, live or fixed tissues, or live animals. The facility has two Zeiss LSM710, each with unique capabilities, and LSM510 META confocal laser scanning microscopes, a newly upgraded Zeiss TIRF scope, PE Spinning Disk scope, Olympus VivaVue live-cell scope with environmental chamber, Olympus wide-field scope, and a Prairie Systems Multiphoton scope for deep tissue and intra-vital imaging. One Zeiss 710 is for general use with 4 lasers and 5 objectives, and is equipped with Definite Focus for long-term image capture. A temperature controller for the stage is also available. The other 710 “BiG” scope has a GaAsP detector for high-sensitivity applications. The Prairie Multiphoton system is quite flexible, accommodating tissue slice and live animal imaging. The system also has software and instrumentation for simultaneous electrophysiology/imaging experiments. To facilitate the production of figures for publication from digital images, image stations are available with MetaMorph Premier, Image J, Volocity 3D, and Zeiss ZEN software.

The Electron Microscopy Service provides a comprehensive electron microscope and surface analysis facility dedicated to bringing state of the art methods in modern imaging, and spectroscopy, to life and materials scientists with all levels of expertise. It is a central facility offering instrumentation, training and service using scanning (SEM & Microprobe), transmission (TEM) and scanning transmission (STEM) electron microscopy, surface analysis (XPS), oxide film growth (MBE) and vibrational spectroscopy (Raman). EM instruments and services are located in two laboratories, one on each side of campus. For the infrequent user, the EMS provides a completely assisted technical support service. For the trained researcher, EMS is an available equipment resource. EMS is staffed with experts in each technique who can teach researchers to operate the instruments, in order to conduct their own measurements. Once trained, expert users have 24-hour access to the instrumentation. The EMS staff can also provide guidance, consultation, and collaboration in the application of our techniques to your specimens. Equipment for life science specimen preparation includes freeze etching, freeze substitution, critical point drying, shadowing/coating and ultramicrotomy. Equipment for materials science specimen preparation includes coating, slicing, disc cutting, polishing, ultramicrotomy, electrochemical and chemical thinning and ion beam milling.

The EMS is a regional center of excellence for atomic resolution STEM. We have upgraded our Scanning Transmission Electron Microscopy (STEM) facility by installing a Nion aberration corrector on the VG HB601UX dedicated STEM and adding a state of the art aberration corrected JEOL ARM-200CF.

Development work is continuing with Physics to build an Ultra Fast Electron Microscope (UEM) that will combine the resolution of a TEM with the temporal resolution of fast laser spectroscopy. In addition to our TEM, SEM and STEM instrumentation we also offer vibrational spectroscopy (Raman), surface analysis (X-ray Photon Spectroscopy) and extensive specimen preparation facilities. Other instrumentation in EMS is a variable temperature, ultra high vacuum scanning probe microscope, and a Molecular Beam Epitaxy system for growing oxide layers.

New MRI for Animal Imaging: The facility is a 2,000 sq. ft. animal imaging laboratory with a new Agilent 9.4 Tesla 30 CM MRI system able to image small animals and samples up to 7.5 cm in diameter. The suite also has space for animal surgeries and short-term housing for animals. An isofluorane anesthesia system, body temperature control and monitoring system for vital signs and gating system (SA Instruments) are installed to permit free-breathing acquisition during quantitative MRI measurements. The system provides full support of MRS and MRI studies in rodents including a complete set of two heavy duty and efficient gradient coils (o.d./i.d.: 205/120 HD, 300A, 600mT/m; and 115/60 HD, 200A, 1000mT/m), three volume Birdcage quadrature coils used to image whole body and organ specific volume (i.d./od.: 39/59, 38/119 and 72/119 mm), two sets of 4 channel phased array coils for acquisition of rodent hearts, prostate and the neurological system. Two multi-nuclei surface coils are also available for image acquisition in rodent tumor models and for the acquisition of magnetic resonance spectroscopy (MRS) data for in vivo biochemical analysis. Advanced MR elastography sequences, utrashort time imaging (SWIFT sequences), and multi-nuclei MRS techniques are being developed. Numerous Radio Frequency coils for different frequencies, protocols and sizes are available. The 11.5 Tesla micro-MRI system (1cm diameter) is also available.

The Flow Cytometry Service (FCS)The Flow Cytometry Service (FCS) provides services for analysis and sorting of cells, as well as training and consultation for the planning and execution of experiments and projects. The FCS operates six flow cytometers and two cell sorters, with an new state-of-the-art Beckman Astrios 5 parameter/16 color high speed sorter housed in a biocontainment hood for sorting live human samples. Analyzers include a BD LSRII Fortessa flow cytometer with four lasers and a high-throughput system for rapid, hands-free acquisition of samples from 96-384 well plates, two CyAn analyzers, and a new Beckman Gallios 3 laser/10 color cytometer. The BioRad Bioplex system is capable of rapidly analyzing up to 35 multiplexed analytes in 96 well plates. The FCS also maintains an automatic magnetic bead sorter (AutoMACS from Miltenyi Biotec) that is often used as a pre-sorter to enrich rare populations of cells before sorting for greater purity on one of our sorting flow cytometers. The services offered by the FCS include training users to run and analyze their samples on their own or assisted analysis, which involves highly trained FCS personnel who would run and analyze samples. Users can register onto the online scheduler (http://schedule.rrc.uic.edu/fcs/) to see and schedule instrument use.

Various applications of flow cytometry include immunophenotyping, intracellular cytokine/protein analysis, measurements of autofluorescent proteins, antigen or ligand density, apoptosis, enzyme activity, cell cycle analysis, DNA and RNA content, membrane potential, analysis of side populations for cancer stem cells, cytokine receptors and its synthesis, drug uptake and efflux, phagocytosis and viability obtained from cells, isolated nuclei, organelles or microorganisms. Changes in cell cycle, intracellular pH, intracellular calcium, intracellular glutathione and oxidative burst can be also detected with these instruments.

The DNA Services facility is part of the Center for Genomic Research. It provides DNA sequencing services using ABI automated capillary sequencing and next-generation instruments. Capillary services include complete sequencing from bacterial cultures, sequencing plasmids, PCR products or other templates provided by users. Sequence chromatograms are analyzed and edited by our staff. The next-gen sequencing facility houses an Ion Torrent Personal Genome Machine (PGM) and new Proton. The PGM can produce over one Gigabase of sequence data with a 2-hr sequencing run at low cost. Approximately 3 million reads of 350-400 bases are produced, and throughput is anticipated to increase every few months as the technology is improved. This machine is ideal for small genome sequencing, amplicon sequencing, targeted resequencing, RNA seq with low complexity transcriptomes, and may also be used for ChIP-seq as well as other applications. The Proton sequencer increases throughput to 15 Gig data per run and, with release of the next generation chip, will be capable of great than 30 Gig, sequencing a human genome for $1,000. Sample prep instrumentation includes GeneX and Eppendorf robots, Covaris shearing device, Pippin Prep and Agilent TapeStation. For Illumina sequencing, the facility does the sample preparation and QC, and sequencing is done with the UIUC Illumina instruments at the core in Champaign.

The facility also offers real time PCR and sequence detection service with four high-end systems providing the ability to perform very sensitive, accurate, and reproducible measurements of gene expression levels. A new LifeTech Quantstudio Digital PCR joins two VaII7s (one with plate autoloader) and a 7500 fast instrument. In addition, the instruments can be used in other applications such as detection of single nucleotide polymorphorisms (SNPs), viral load measurements for clinical purposes. High-throughput analysis is available with 384 well plates or TILDA microfluidic cards. After an initial training session, users are able to run and analyze their own experiments. An additional workstation with appropriate software is also available to assist with primer and probe design.

The Core Genomics Facility (CGF), also part of the Center for Genomic Research, provides expertise and instrumentation for the analysis of genotype, gene expression, and epigenetics. Affymetrix GeneChip services include array hybridizaton and data acquisition, hybridization and scanning of glass slide DNA arrays, specialized software for data acquisition and analysis, and bioinformatics support. Cytoscan array processing and analysis is available for digital cytogenetics. The latest Affymetrix high-throughput gene array instrument, the Gene Titan system, processes 16 to 96 genotyping or gene expression arrays per run. It has the ability to run the latest Affymetrix 2.2 million element genotyping arrays and inexpensive gene expression chips. The MassARRAY Analyzer 4 system from Sequenom offers the power of mass spectrometry and advanced data analysis tools to meet the needs of high to low throughput genetic screening. It is capable of multiplexing up to 40 SNPs in 384 samples per run at very low cost per SNP. The lab offers services for SNP genotyping, somatic mutations and copy number analysis, quantitative gene expression and methylation analysis. Software solutions for data acquisition, quantification and data analysis are available.

Center for Research Informatics: The RRC informatics initiative is part of a new center under the direction of the Chief Research Informatics Officer with a staff of 18. The bioinformatics support group consists of two Phd and two Masters level informaticians who provide analysis of next-gen sequencing, qPCR, microarray, and proteomics data. Two systems operations IT staff support informatics as well as the Biorepostory and the central High Performance Computing Cluster. Other staff develop and maintain the CCTS Clinical Data Warehouse, perform clinical research analysis, text mining, etc. The RRC and VCR expanded research server, storage and data pipeline capabilities with a 3000 core HPC cluster that includes 3 high-memory nodes dedicated to genomic research. A smaller 200 core/GPU mixed cluster is also used to house the Galaxy environment and a set of genomic analysis tools.

Biospecimen Repository: The RRC collaborated with the Department of Pathology to develop a comprehensive, university-wide processing lab and repository for research tissue banking. The University provides support for researchers submitting samples to the facility for processing and storage. A new laboratory and freezer farm have been fully equipped. Patients entering the hospital are asked for consent to store and use their tissues for research purposes. Investigator-initiated protocols are also supported. Solid tissues, blood, and any other tissues are processed and preserved at -85 or -156deg in a secure facility with redundant, computer controlled temperature monitoring. The facility can also process samples to obtain live cells or nucleic acids for investigators.

Pathology/RRC Research Histology and Tissue Imaging Core The Research Histology and Imaging Core facility is a collaboration between the RRC and the Department of Pathology. The histology lab is a fully functioning state of art Research Histology Core providing processing, sectioning, routine and special stains along with immuno-histochemical procedures for human and experimental animal tissues. Dr. Peter Gann has academic responsibility for lab. The Laser Capture Microscope Aperio and Vectra Tissue Imaging System are located adjacent to the Histology lab. The Vectra system is capable of imaging and quantitation of up to 5 fluorescent probes in fixed tissue. The system employs spectral unmixing to obtain highly accurate quantitative data, and sophisticated machine learning to identify and analyze structures of interest.

Center for Structural Biology (CSB) The Center for Structural Biology (CSB) was established to provide access to instrumentation used in biophysics and structural biology research. The main component of the CSB is the NMR facility, which houses four high field nuclear magnetic resonance (NMR) spectrometers operating at 600, 710 (solid state), 800 and 900 MHz proton frequencies. The 600 and 900 MHz NMR spectrometers are equipped with cryogenic probes, affording maximal instrument sensitivity. The 800 MHz NMR spectrometer operates with a standard "room temperature" probe which allows for a greater range of sample temperatures and facilitates more demanding experiments such as those used to study diffusion or relaxation. Other instrumentation housed in the Center include a differential scanning calorimeter (DSC), isothermal titration calorimeter (ITC), a circular dichroism (CD) spectropolarimeter, and analytical ultracentrifuge.

The Macromolecular Structure Facility (MSF) x-ray diffraction instrument has been integrated into CSB. In addition, four constant temperature chambers, computer, crystallization kits, and a microscope have been purchased with funds from CCTS to support x-ray crystallography. The chambers are located in the HTS core to facilitate robotic set up. Although the instruments in the CSB are optimized for the study of proteins and nucleic acids, we are capable of analyzing a wide variety of samples and contributing to research programs in many different fields. Indeed, the CSB instruments are utilized for research in chemical, engineering, materials and pharmacological research.

The Mass Spectrometry, Metabolomics & Proteomics Facility (MMPF) serves as a research core facility and resource for the analysis of a wide variety of molecules ranging from low molecular weight volatile compounds to high mass polymers and biopolymers such as proteins. Types of measurements include qualitative and quantitative analysis, purity assessment, molecular weight determination, and high-resolution exact mass measurements for the determination of elemental composition. The facility has 14 Mass specs in two campus locations. A Thermo LTQ Orbitrap Velos joins the Thermo LTQ-ICR-MS for accurate mass proteomics. An Agilent Chip-Cube LC system, an “LC on a chip”, has been adapted for use with the Orbitrap. This system greatly reduces MS run time for protein separations as well as increasing sensitivity. In addition to two Agilent 6410 triple quadrupole instruments the lab has added AB Sciex 5500 and 6500 Qstars for small molecule analysis. The 6500 is used for lipids, lipidomics as well as other applications requiring highest precision, sensitivity and speed. Full service sample preparation is available for proteomics and metabolomics with a fully-equipped sample preparation laboratory and staff.

The East campus Lab houses a GC-Mate GCMS, the ABI 4700 MALDI TOF/TOF used for MS imaging, as well as proteomics, and a Waters SCF-MS (Supercritical Fluid-Mass Spectrometer) enables a combined technique in which a mixture of analytes can be separated into solutions of individual components by supercritical fluid chromatography.

The NMR and microMRI Lab provides service and, more commonly training, to use its equipment. Inexperienced and practiced NMR and MRI users receive a lecture on the technique and policies of the lab then supervised hand-on practice ensures that new users can confidently utilize the equipment. The lab has a 500 MHz and 360 MHz NMR instruments and is available 24/7/365. All data can be up loaded for off line analysis and archiving. Scheduling is arranged via RRC web accessed software (OLISS).

The lab has a 500 MHz NMR with a 54 mm bore magnet operating as a microMRI or a multinuclear NMR spectrometer. MRI can analyze samples up to 10mm in diameter or smaller than 1mm. The NMR uses direct or indirect detection with Z gradient capabilities. Temperature control is available, precise to 0.1 degree C. The variable temperature can use either liquid nitrogen or an air chiller for moderate cooling. The 500 for spectroscopy has a 5mm Bruker BBO probe, a 5mm Nalorac inverse detection probe with H1 observe and C13 and N15 decoupling and a 2.5mm Bruker TXI with H1 observe and C13 and P31 decoupling. The 500 for imaging has probe having a 5mm H1 RF coil, a 10mm H1 RF coil and a 5mm dual Na23/H1 RF coil. The 500 for MR Elastography has a 10mm H1 RF coil. The 360 has a 5mm QNP probe able to observe H1, F19, C13 and P31 without tuning and variable temperature control to 1C. Dr. Kleps has collaborated with researchers in Departments of Biochemistry, Bioengineering, Chemical Engineering, Chemistry, Hematology, Medicinal Chemistry, Neurosurgery, Pharmacognosy, Physics, Physiology, Surgery and several outside laboratories.

High Throughput Screening facility: The premise of HTS is to automate and miniaturize the assay process, thereby significantly decreasing the cost and time commitments of screening a biological target against thousands of chemical compounds. The core houses a Tecan Freedom EVO 200 liquid handling robot that is fully capable of assembling and monitoring over 10,000 reactions, in duplicate, in a typical working day. A newly acquired Tecan Infinite F200 spectrophotometer is fully integrated into the robot deck to capture absorbance, fluorescence, and luminescence output from the assays. Once the screening and data collection are completed, the results are analyzed to generate a structure-activity relationship for the screened compounds, identifying chemical trends in the compounds that affect or inhibit the biological target of interest.

The HTS facility currently offers a library of over 100,000 diverse, drug-like compounds available for screening. Our most recent purchases include the Chembridge DIVERSet™ library (50,000 compounds), the Maybridge HitFinder library (14,400 compounds), and the Prestwick Chemical Library (1,200 marketed drugs). Researchers at UIC who wish to deposit novel compounds or natural product fractions into our collection are encouraged to do so. The Tecan Freedom Evo 200 is also ideally suited to carry out high-throughput protein crystallization. Users can typically screen over 1000 crystallization conditions in under 2 hours. The HTS facility is stocked with 25 unique crystallization suites each containing 96 different conditions.

The Protein Research Laboratory (PRL) provides comprehensive services related to protein studies. Services include peptide synthesis, protein sequencing, protein purification, antibody production, amino acid analysis, western blotting, PCR, ELISA, circular dichroism spectroscopy, 1-D and 2-D gel electrophoresis, proteomics, and recombinant protein production. Major instruments include peptide synthesizers, a Jasco 710 circular dichroism spectropolarimeter; a Micro-Tech MicroLC HPLC system; an HP1100 HPLC system with variable-wavelength UV-visible, photodiode array, fluorescent, light-scattering and mass spectrometric detectors; 2-D SDS-PAGE systems; a BioRad Chemi-Doc system fluorescent gel imager with a cooling CCD camera; a Bio-Rad Proteomeworks System including high-throughput 2-D gels, a Gel Spot Cutter and a Bio-Rad FX Pro Plus Multi-Imager; a Hybaid PCR machine with temperature gradient; an Awareness Tech ELISA reader; a Linde liquid nitrogen cell storage system; and an Olympus fluorescent inverted microscope. All services include consultation and assistance according to the researcher’s needs.

The Transgenic Production Service (TPS) generates transgenic and gene-targeted mice. Services include pronuclear microinjection of DNA constructs into mouse zygotes for the production of transgenic founders and injection of targeted ES cell lines into blastocysts to produce chimeric mice. Investigators submit purified transgenes or targeted ES cells for microinjection to produce founders or chimeras, respectively. Vectors may also be submitted to the facility for gene targeting in ES cells. Services for cryopreservation and storage of embryos and sperm are also offered to provide insurance against the loss of a colony or to preserve seldom-used strains. Frozen strains may be recovered using IVF and embryo transfer. The facility maintains a Leitz Diavert inverted microscope fitted with a range of phase contrast and HMC objectives, mechanical inertia-free Leitz manipulators and an Eppendorf microinjector. Other equipment includes a micropipette-puller and microforge for fashioning microinjection and embryo-transfer needles, a Leitz Zoom stereomicroscope for embryo collection and surgical procedures, and a Thermo Forma CO2 incubator for embryo culture. For ES cell targeting the facility houses a Bio-Rad Gene Pulser (electroporator), a NuAire Labgard Class II, Type A2 laminar flow hood, and a dedicated Thermo Forma CO2 incubator. Storage of frozen embryos and sperm, as well as ES cell lines is provided by a Custom Biogenic Systems (CBS) LN2 Isothermal Vapor Storage System.

Physiology Core, Center for Cardiovascular Research: The core contains a surgical suite equipped with Zeiss Dissecting Microscopes, Harvard ventilators and isoflurane vaporizers. We have experience in producing both acute and chronic murine models of cardiovascular and cardiopulmonary disease. A Visual Sonics Vevo 770 high-resolution ultrasound imager is available for cardiovascular measurements and for tissue/organ screening.

In addition to the Research Support Services, the RRC provides technical support in the form of a Scientific Instrument Shop and the RRC Scientific Supply Center. The SIS repairs and maintains electronic equipment and designs electronic devices to the specifications of campus investigators’ research needs. It repairs, designs and constructs physical devices and machinery to investigators’ specifications as their research needs require. The RRC Scientific Supply Center carries a wide array of items that are sold at a discount from many major vendors. Freezer programs for instant access to media and enzymes include all major brands.