2013 - vanderbilt university medical center core handbook... · individual investigators. expertise...
TRANSCRIPT
2013
DATE OF PUBLICATION
Cores and Shared Resources offer access to a wide array of cutting-edge technologies, high-end instrumentation, technical support and training, as well as reagents and special products you need to conduct your research.
VUMC Core Facilities and Shared Resources are available to all graduate students, postdoctoral fellows and principal investigators. Each core is a shared laboratory resource that provides a cost-effective way to conduct high-quality state-of-the-art research.
The listings in this handbook provide more details about selected shared resources, including services and technology available and how to contact the shared resource scientists.
A complete list of cores and shared resources is available at www.mc.vanderbilt.edu/CFUIS .
Core Service Fees and Funding Support
While user fees are charged for services and products provided by cores and shared resources, there is funding available to help you pay for core services. The Vanderbilt Institute for Clinical and Translational Research (VICTR) offers micro-grants for purchasing core services and products, as well as pilot project funding.
Go to www.mc.vanderbilt.edu/starbrite to get started.
Advanced Computing Center for Research & Education (ACCRE)
ComputingCluster:CarieLeeKennedy;StorageDevelopment:AlanTackettSteeringCommittee:DavePiston,VUMC;RonSchrimpf,VUSE;PaulSheldon,A&Sȟ #ÈÁÉÒ
What we can do for you:
Research computing cluster
Disk storage on GPFS cluster file system and in depots
Custom gateway servers
Tape backup service
ACCRE is most widely known for its shared research computing cluster and disk storage on the GPFS cluster file system. Cluster usage is based on researcher contributions to the shared cluster. Researchers can pay for disk storage quotas in the /data partition which is backed up to tape or on the /scratch partition which is not backed up to tape. Disk storage is also available in storage depots. Some research groups also have custom (or private) gateways for use with the cluster. The center also operates a tape backup system to back up data on custom gateways and remotely from labs on campus.
Contact Information Website: www.accre.vanderbilt.edu Email: [email protected] Phone: (615) 322-7256 OR (615) 343-2244
Acknowledgment Text This work was conducted in part using the resources of the Advanced Computing Center for Research and Education at Vanderbilt University, Nashville, TN.
Location Hill Center Suite 2011231 18th Avenue South
Biostatistics Collaboration CenterCoreManager:SethMartinCoreDirector:JeffreyBlume
What we can do for you:
The BCC offers statistical and computational collaboration for:
Database construction
Data management
Data display and summarization
Statistical analysis techniques for bench and clinical sciences
Sample size projections
Experimental design
Study reporting
Manuscript and poster preparation
Grant preparation
For training, please send an email to: [email protected]
To schedule services, please send an email to: [email protected]
The Biostatistics Collaboration Center (BCC) at Vanderbilt is a university sponsored core resource whose goal is to provide for, enhance, and facilitate statistical collaborations involving the design, conduct, analysis or publication of biomedical research at the university. The BCC is comprised of biostatisticians and computer systems analysts from the Department of Biostatistics who have considerable expertise in the application of statistical methodology to clinical and bench sciences, and who are available to design experiments using modern statistical techniques. BCC personnel typically work under the supervision of Biostatistics faculty to meet the needs of clients. The BCC has considerable expertise in the design, conduct, and analysis of large-scale clinical trials as well as experimental designs for basic biomedical research. Varying levels of expertise are available for consultation, from bachelors and masters level trained biostatisticians and computer systems analysts to full professors.
Contact Information Website: www.vanderbilt.edu/biostatistics/ Email: [email protected] Phone: (615) 875-6914
Location S-2323, MCN
BioVU Core Manager: Erica Bowton and Jennifer Madison
Core Director: Jill Pulley
What we can do for you:
Provide access to banked DNA samples linked to de-identified clinical records.
Services include removing samples from storage and plating of the samples for genetic studies.
For training and scheduling, please email: [email protected]
BioVU is the Vanderbilt DNA biorepository of DNA extracted from discarded blood collected during routine clinical testing and linked to information in the Synthetic Derivative. The DNA is de-identified and then linked to de-identified clinical data in the Synthethic Derivative creating a centralized resource for making associations between genetic information and disease susceptibility or variable drug responses across populations. As BioVU grows, genotyping data is continuously re-deposited back into the database.
Contact Information Website: https://starbrite.vanderbilt.edu/biovu/ Email: [email protected] Phone: 615-875-7609
Acknowledgment Text The dataset(s) used for the analyses described were obtained from Vanderbilt University Medical Center's [INSERT: Synthetic Derivative or BioVU] which is supported by institutional funding and by the Vanderbilt CTSA grant ULTR000445 from NCATS/NIH.
Location 2525 West End Ave, Suite 600
Cardiology Core Lab
For Clinical and Translational Research Core Director: Yan Ru Su M.D.
What we can do for you:
1. Vanderbilt Heart Tissue Bank/Biorepository. We provide flash frozen,
OCT and paraffin sections of human heart and vascular tissues for basic
and translational cardiovascular research.
2. Biomarker assay using Luminex 200 technology. We offer multiplex
biomarker assay or ELISA assay for cardiovascular disease related
biomarkers.
3. Blood sample processing for investigator initiated clinical studies
4. RNA and DNA extractions from blood/tissues.
The mission of Cardiology Core Lab is to provide the best resources support for cardiovascular
translational and clinical research to faculty members and trainees on campus. The well-established
VHVI Heart Registry/Bio-repository have collected significant number of patient’s plasma, serum,
DNA, explanted heart, apex of the heart and valve tissues supplemented with long term follow up
clinical information. We also provide experimental and biological sample processing service to
Vanderbilt investigators. We aim to fostering the development of 1) platforms for the discovery of
the molecular mechanisms of CVD; 2) robust engines for clinical and translational research; and 3)
genotypes and clinical phenotypes requisite for pharmacogenetics and personalized cardiovascular
medicine.
A. Mitral Valve
VHVI 00743 VHVI 00790 VHVI 00791
B. Carotid Artery
C. Apex from VAD
Contact Information
Website: http://www.vanderbilthealth.com/cardiovascular/23792?previewsession=1
Email: [email protected]
Phone: (615)-936-2574
Location:
319 PRB
Cell and Developmental Biology Equipment Resource Core Core Manager: Anthony Tharp, PhD Core Director: William Tansey, PhD
What we can do for you:
Autoclaves Dishwashers and Dryers
Ice Machines Ultrapure Water
Gel Documentation Systems Scintillation Counters
Gamma Counters Ultracentrifuges
High Speed Centrifuges Thermocyclers
qPCR Thermocycler Incubator Shakers
SpeedVacs Freeze Dryer
RNA Baking Oven Odyssey
Synergy Plateready Typhoon Phosphorimager
LAS4000 Chemiluminescent Imager Film Processors with Dark Rooms
Particle Counter EVOS FL Inverted Microscope
Sakura Cryostat Nanodrops
Nikon Spinning Disk Confocal (CDB Faculty only)
Leica Confocal (CDB Faculty only)
For training: Send an email to [email protected] or call 615-322-8326 Scheduling: Use C.O.R.E.S. website to Reserve Core Device or call 615-322-8326
The CDB Equipment Resource Core provides a wide variety of instruments to support the daily research needs of your lab. Except for our confocal microscopes, all services are open to the entire Vanderbilt community. Some of our equipment is free to use and some is charged on a pay-per-use basis. A complete listing of equipment and their location and any associated fees can be found on the CDB Equipment Resource website. Training for all of our CDB equipment is free to any user.
Contact Information Website: http://www.mc.vanderbilt.edu/cdb/equipment-resources Email: [email protected] Phone: (615) 322-8326
Acknowledgment Text The Vanderbilt University Cell and Developmental Biology Equipment Resource Core provided instrumentation and/or analytical support for these studies.
Location U-3202 MRB3 3rd and 4th floor of MRB3 2nd floor of MCN
Cell Imaging Shared Resource (CISR) Core Manager: Sean Schaffer Core Director: Sam Wells, PhD
What we can do for you:
• Confocal Microscopy • Specialty Laser-Scanning Microscopy • Wide-field (Conventional) Microscopy • Specialty Wide-field Microscopy • Transmission Electron Microscopy • Environmental Scanning Electron Microscopy • General Electron Microscopy Processing • Image Processing and Analysis Assistance • Live Cell Support - Stage Incubators and Ventilators
New User Information & Training: https://cisrweb.mc.vanderbilt.edu/CISR/site/newuser.php
Scheduling: https://cisrweb.mc.vanderbilt.edu/cellimaging/index.php
The CISR is a shared resource for advanced microscopy and quantitative imaging (both optical and EM), available for all researchers with Vanderbilt University appointments. We provide expert training and consulting on the proper use and techniques of all of our instruments and offer guidance to facilitate the development of basic and advanced imaging skills. We offer a fully equipped EM facility able to handle all aspects of EM sample processing from embedding, sectioning and staining to critical point drying sputter coating, along with both TEM and ESEM imaging.
Contact Information Website: https://cisrweb.mc.vanderbilt.edu/CISR/ Email: [email protected] Phone: (615) 343-3750 or 936-3706
Location 742 Light Hall - Main Optical Facility T3208 MCN - EM Preparation Lab
Acknowledgment Text Style I. The minimum acceptable acknowledgement should read: 'Experiments/Data analysis/presentation [include what you use]' were performed in part through the use of the VUMC Cell Imaging Shared Resource.
Style II. If space permits, please append the following list of grant numbers: 'Experiments/Data analysis/presentation [include what you use]' were performed in part through the use of the VUMC Cell Imaging Shared Resource (supported by NIH grants CA68485, DK20593, DK58404, HD15052, DK59637 and EY08126).
Center for Human Genetics Research: Computational Genomics Core
Faculty Directors: Jonathan Haines PhD, William Bush PhD and Bingshan Li PhD
What we can do for you:
Software development - We build and host, custom applications to store, analyze, and annotate genetic/clinical study data.
Statistical Analysis - We provide custom statistical advice, analysis, and method development for genetic study data
IT Infrastructure - We provide the informatics, system administration, data, and project infrastructure for genetic studies
Bioinformatics - We provide standard and custom bioinformatic analysis for next generation sequencing and genotyping studies
This core provides access to information technology and data analysis expertise for activities related to genetics research. The information technology component provides the necessary database development expertise to assist a wide variety of projects. It also provides development expertise for creating web application interfaces for databases as well as standalone applications that encapsulate new statistical methods for analyzing genetic data. The statistical analysis component provides the necessary expertise to analyze genetic data generated at Vanderbilt or externally by cores or individual investigators. Expertise in family based, case/control, GWAS (genome-wide association study), DNA sequence data (whole exome/whole genome), linkage, linkage disequilibrium, association, and risk factor analyses is provided. Access to a centralized database and to all the necessary software is also provided.
Contact Information Website – chgr.mc.vanderbilt.edu/page/computational-genomics-core Email –[email protected] Phone – 615-343-2607
Acknowledgment Text for Abstracts, Papers, and Talks The Vanderbilt University Center for Human Genetics Research Computational Genomics Core provided software development, computational, and/or analytical support for this work.
Location 1207 17th Ave South, Ste 300
Center for Human Genetics Research: Genetic Studies Ascertainment Core (GSAC)
Core Manager: Renee Laux, MS
What we can do for you:
Genetic Study Design, Development, and Management
IRB Development and Monitoring
Participant Ascertainment
Data Management
Educational Activities and Community Outreach To schedule a consultation, please email [email protected]
Ascertainment for genetic studies is a crucial and labor-intensive effort. The GSAC has the expertise to assist investigators in developing a successful ascertainment program. We aid in the development and coordination of both individual and family based genetic studies. We perform various tasks associated with ascertainment, including developing IRB proposals, obtaining consent, taking family and medical histories, performing exams, obtaining biological samples and performing data management. We assist with the hiring and/or training of personnel to perform ascertainment for you if that better meets your needs. We also provide materials necessary for ascertainment, including blood and buccal swab kits. We currently work on a variety of different disorders.
Contact Information Website – http://chgr.mc.vanderbilt.edu/page/genetics-studies-ascertainment-core. Email – [email protected] Phone - 615-322-6960
Location 1207 17th Avenue South, Suite 100
Clinical Research Center Core Lab Angie Sneed, MBA, MT, Laboratory Manager
What we can do for you:
The following analyses are currently available: HPLC Catecholamine (P, U) DNA Extraction (B) Total Nitrogen (U) ELISA:
o Cortisol (Sal) o Cystatin C (U) o Estramet (U) o Legionella (U) o Melatonin (Sal)
Nt-proBNP (P) 6-Sulfatoxymelatonin (U)
* B = Blood, P = Plasma, S = Serum, Sal = Saliva, U = Urine
The Vanderbilt Institute for Clinical and Translational Clinical Research Center Laboratory, a CAP/CLIA certified laboratory is available for your research assay testing needs. A diverse team of technologists and instrumentation specialists with over fifty years of combined experience are here to assist you.
Acknowledgment Text Publications that result from VICTR support should reference the grant. By accepting VICTR support you agree to include the following citation in your publications: "Supported in part by Vanderbilt CTSA grant UL1 TR000445 from NCRR/NIH"
Location Medical Center North A-3219 & AA-3231
Contact Information Website: www.mc.vanderbilt.edu/crc Email: [email protected] Phone: 615-322-3011
Clinical Trials Center Jill Janssen, Director
What we can do for you:
Services provided by the Clinical Trials Center to Vanderbilt investigators include but are not limited to: Provide Research Personnel Preparing, submitting and maintaining IRB documents Review, development and negotiation of study budgets Facilitate contract negotiation Serve as a resource center for Investigators, Sponsors, Research Nurses
and Volunteers. Provide complete clinical trial management
Our Mission: To take the burden away from clinical research and to provide the services needed to allow any faculty who would like to participate in clinical
trials, to do so.
Contact Information Email: [email protected] Phone: 343-8010
Location Village at Vanderbilt Suite 3500
CSB Biomolecular NMRCoreManager:MarkusVoehler,Ph.D.CoreDirector:MarkusVoehler,Ph.D.
What we can do for you:
The principal mission of the Biomolecular NMR Center is to provide instrumentation for, and aid in obtaining data on the structure and dynamics of biological macromolecules. The facility offers state-of-the-art instrumentation, training, software and assistance in designing experiments. We strive to help the Vanderbilt community realize the potential of biomolecular NMR and to work with NMR spectroscopists to stay current with the most recent experimental approaches.
Scheduling: Please submit a brief description of your project on the
CSB outreach page: http://structbio.vanderbilt.edu/access.php
The facility offers state-of-the-art instrumentation including a 500 MHz, two 600 MHz, a 800 MHz and one 900 MHz AV-III spectrometers. All instruments are equipped with four channels, 1H, 13C, 15N and 2H, using the latest cryoprobe technology to drastically enhance the sensitivity. We further offer 31P capability and two SampleJets for high-throughput screens. A variety of training opportunities are offered as well as assistance with software and experimental design.
Contact Information Website: http://structbio.vanderbilt.edu/nmr/ Email: [email protected] Phone: (615) 322-1573 OR (615) 322-1570
Acknowledgment Text By accepting Biomolecular NMR Facility support you agree to include the following citation in your publications: 'Supported in part by MRI grant #0922862 from NSF, SIG grant #1S-10RR025677-01 from NIH and Vanderbilt University funds'
Location VUBNMR 009
CSB Biophysical InstrumentationCoreManager:LauraMizoueCoreDirector:WalterChazin
What we can do for you:
We provide new user training on 4 instruments: CD spectropolarimeter Differential scanning calorimeter Steady-state fluorometer equipped with polarizers Isothermal titration calorimeter
Unassisted access to instruments is provided upon completion of training To arrange for training or schedule time on an instrument, please email:
The Center for Structural Biology maintains a variety of instruments for studying the conformation/stability of macromolecules and for measuring the affinity/ thermodynamics of biomolecular interactions. We provide individual training for new users, after which access is self-served. Please visit our website for more information or set up an appointment to discuss your research project.
Contact Information Website: http://structbio.vanderbilt.edu/wetlab/instrumentation.php Email: [email protected] Phone: (615) 936-2253
Acknowledgment Text CD/Fluorometry/Calorimetry experiments were performed in the Biophysical Instrumentation Core which is supported by the Vanderbilt Center for Structural Biology.
Location 5141, MRB III 5147, MRB III
Division of Animal Care Core Manager- Tina Melendy, Accounting Assistant II
Director- Dr. Jeanne Wallace, DVM, DACLAM, Asst. Vice Chancellor for Research, Assoc. Professor of Pathology/Comparative Medicine
What we can do for you:
The Division of Animal Care (DAC) is the service core that provides procurement,
husbandry, and healthcare for experimental animals, as well as scientific/technical support
for VU researchers.
OUR MISSION
To provide humane animal care that meets the highest national standards supporting
knowledge and discovery through research.
WHO WE ARE
We are a dedicated team focused on ensuring humane animal care and use of research
animals. We consist of three main program elements: Husbandry & Animal Care, Veterinary
Care, Comparative Pathology and Business Administration.
Training: https://www.vacup.us/dac/training-sops
Office Hours: 7:30- 4:30 M-F
(615-322-2231) AA6206 Medical Center North (After hours voicemail provides additional contacts)
FAQ: https://www4.vanderbilt.edu/acup/dac/faq.php
Animal Procurement
[email protected] https://dac.mc.vanderbilt.edu/eSirius/index.htm
Animal Transfers/Shipping
[email protected] [email protected] https://sitemason.vanderbilt.edu/site/aVNb2M/animal-transfer
Billing & Rates [email protected]
Contact Information Email: [email protected]
Location Medical Center North AA-6206
Eicosanoid Core Laboratory Core Manager: Ginger L. Milne, Ph.D.
What we can do for you:
Available assays: Isoprostanes Isofurans Neuroprostanes Prostaglandins and their Urinary Metabolites Urinary Leukotriene E4 20-HETE Epoxyeicosatrienoic acids (EETs)
Contact Information Website: www.mc.vanderbilt.edu/eicosanoid Email: [email protected] Phone: (615) 936-5611 or (615) 936-2050
Acknowledgment Text Analysis of eicosanoids (include specific compounds such as isoprostanes, prostaglandins, or leukotrienes) was performed in the Vanderbilt University Eicosanoid Core Laboratory.
Location 502 RRB 561 PRB
Eicosanoid is an umbrella term used to describe any oxidized derivative of arachidonic acid, a ubiquitous polyunsaturated fatty acid (PUFA) in humans. Arachidonic acid can be oxidized in vivo via both enzymatic and non-enzymatic mechanisms to yield bioactive lipid mediators that are of central importance to human physiology and pathophysiology. The Eicosanoid Core Laboratory is a Vanderbilt University Shared Resource designated for the analysis of isoprostanes, prostaglandins, leukotrienes, and their metabolites. All of the assays performed are validated highly precise, accurate, and sensitive mass spectrometric assays.
Epidemiology Biospecimen Core Core Manager: Regina Courtney
Core Director: Qiuyin Cai
What we can do for you:
• Biological sample processing • Biological sample banking • Biological sample aliquoting • Biological sample collection kits • DNA/RNA extraction • DNA/RNA sample banking • Genotyping • Gene expression analysis • Immunohistochemistry staining • Protocol development for biological sample collection and storage, genotyping,
and biomarker assays • Other services that support molecular epidemiological studies
For training, please email: [email protected]
For scheduling, please email: [email protected]
The Molecular Epidemiology Laboratory is led by Dr. Qiuyin Cai and provides genotyping and other lab services for large-scale studies. The Molecular Epidemiology Laboratory provides services to Vanderbilt investigators related to biological specimen collection and storage, as well as biomarker and genetic marker assays.
Contact Information Website: http://medicineandpublichealth.vanderbilt.edu/center.php?userid=1579214&id=33666561#molecular
Email: [email protected] Phone: (615) 936-1351 or (615) 936-0467
Acknowledgment Text Please place the type(s) of services used at our facility at the beginning of the following sentence. Sample preparations/Biomarker assays/Genotyping/……/ were performed at the Survey and Biospecimen Shared Resource, which is supported in part by the Vanderbilt-Ingram Cancer Center (P30 CA068485).
Location B-2104, MCN B-2103, MCN
Epithelial Biology Center Imaging Resource Joseph Roland, Ph.D. – Managing Director
What we can do for you:
High-resolution, automated scanning and analysis of tissue sections, tissue microarrays, and cultured cells (IHC and IF)
Short and long-term live imaging (BF and IF) in a temperature and CO2-controlled environment.
Deconvolution microscopy – fixed and live cell
Colony counting in agar, Matrigel, etc.
Training / Scheduling: Contact Joseph Roland ([email protected])
The Epithelial Biology Center Imaging Resource provides specialized microscopy assistance such as automated slide scanning and analysis, colony
counting, long-term live imaging and deconvolution. The core is capable of high-resolution automated and semi-automated imaging and quantification of
a wide range of cell culture and tissue samples, such as whole pathological samples and tissue microarrays. Whether they are processed for histological,
immunohistochemical, or immunofluorescent studies, expert assistance is offered in planning experiments and processing data in a consistent, objective, and timely manner. The automated imaging and analysis
performed by this core saves researchers and staff weeks of tedious work. An additional service offered by the EBC Imaging Resource is the creation of
digital archives of critical and irreplaceable tissue samples, a benefit only feasible due to the automated high-resolution imaging of whole 25mm x 75mm microscope slides.
Contact Information Email: [email protected] Website: http://www.mc.vanderbilt.edu/root/vumc.php?site=EBC Phone: 322-0686
Location Room 10420, MRB IV
Flow Cytometry Core Scientific Director: James Crowe, Jr Manager Director: Kevin P. Weller
What we can do for you:
Cell Sorting – 3 FACS Aria III’s, with 405nm, 445nm, 488nm, 561nm, and 635nm lasers (up to 15 colors simultaneously)
Analytical Cytometry – 3 LSRII’s with 355nm, 405nm, 488nm, 531nm, 561nm and 635nm lasers (up to 17 colors simultaneously)
Flow CytometryTraining - Beginning to Advanced
Magnetic Sorting - Automacs
Cytof Mass Cytometer-High content analytical Cytometry
Tali Cell Coutner – Red and Green fluorescence with hemocytometer count Amnis Imaging Cytometer-basic imaging plus analysis
Online Scheduling - Core Ordering & Reporting Enterprise System (CORES) https://cfuis.mc.vanderbilt.edu/login.cfmd
We enjoy state-of-the-art digital instrumentation maintained at the highest standards we can attain. This quality control allows researchers to sort cells at high efficiency and purity under the proper conditions or to run analytical experiments with as many as 17 different fluorochromes simultaneously. We are dedicated to providing the best service and training possible to ensure the best results attainable for our research scientists and physicians. Please visit out website and feel free to contact us with questions or to set up an appointment to discuss your research project.
Contact Information Website – www.vmcflow.com Email – [email protected] Phone - 615-343-8323
Acknowledgment Text "Flow Cytometry experiments were performed in the VMC Flow Cytometry Shared Resource. The VMC Flow Cytometry Shared Resource is supported by the Vanderbilt Ingram Cancer Center (P30 CA68485) and the Vanderbilt Digestive Disease Research Center(DK058404)." .
Location Medical Center North T-0101
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Hormone Assay & Analytical Services Core
Core Director: Owen McGuinness, PhD Core Manager: Dale Edgerton, PhD
What we can do for you:
Hormones: Insulin, Glucagon, Catecholamines (epinephrine & norepinephrine), Cortisol, Corticosterone, Leptin, Growth Hormone, C-peptide, ACTH, Aldosterone, Ghrelin,T3,T4, Estradiol, Testosterone, Progesterone
Amino Acids and Gluconeogenic Assessment
Luminex Applications: cytokines (Il-6, TNF Alpha, MCP-1), adipokines (adiponectin and resistin), cardiac markers, and many others
Nucleotides: AMP, ADP, ATP, ZMP and cAMP
Lipids/Lipoproteins
Isoprostanes (Oxidative Stress Metabolites):F2-isoprostanes and the major urinary isoprostane metabolite (2,3-dinor-5,6,-dihydro-15-F2t-IsoP,F2-isoprostane-M)
The Hormone Assay & Analytical Services Core is a support laboratory at VUSM administered by the Vanderbilt DRTC and MMPC. The primary objective of the core is to provide sensitive, inexpensive, and reproducible analyses to investigators that facilitate all types of diabetes related research. These analyses include measurement of stable isotopes, oxidative stress assessment, lipids, amino acids, purine nucleotides and hormones in biologic fluids as related to diabetes, endocrine and metabolic research. Secondarily, the Hormone Assay & Analytical Services Core offers regional access to assays not otherwise available. In addition to technical support, the Hormone Assay & Analytical Services Core provides training to other lab personnel as to the methods, interpretation of results and advises on advantages and limitations of various procedures. The core provides space, equipment, and personnel for sample analysis and method development. Investigators pay a fee-for-service that covers the cost of reagents, supplies, a percentage of personnel salary, and pro-rated service contracts. It provides a valuable resource for all investigators without ready access to wet-lab research space and personnel. The services provided utilize modern instrumentation run by experienced research assistants in a reliable, quality-controlled environment.
Contact Information Website: http://hormone.mc.vanderbilt.edu or http://www.mc.vanderbilt.edu/diabetes/drtc/cores/hormone_assay/index.phpEmail: [email protected] Phone: 615-936-1624 or 615-343-3193
Location 713, 717, & 753 PRB
Acknowledgment Text Investigators publishing data obtained from the core are requested to provide the following publication credit: Hormone Assay & Analytical Services Core, Vanderbilt Diabetes Research and Training Center supported by NIH grant DK20593. The Hormone Assay & Analytical Services Core is also a support core for the MMPC. For all mouse related publications and/ or presentations containing core data please credit Hormone Assay & Analytical Services Core, MMPC, Vanderbilt University supported by NIH grant DK59637.
Information Technology Services Core Manager: John McCammon Core Director: Esfandiar Zafar
What we can do for you:
High Performance Network Storage
• Blue Arc electronic file storage
• Snapshot file recovery
ITS has established a high-performance network attached storage (NAS) environment for research data storage. The system uses Hitachi disk and BlueArc's Titan SiliconServer to offer 231 TB (as of January 2012) of high-performance storage. Space (virtual volumes) on the system can be mounted via CIFS, NFS, or both. The system has native addresses on the University 129.59 network, the Med Center 160.129 network, and the ACCRE 10-dot network, giving unfirewalled access to all parts of Vanderbilt. The system uses VUnetID authentication. Data on the system are backed up to tape, and an optional snapshot service also provides for file recovery.
Contact Information Website: http://its.vanderbilt.edu/ Email: [email protected] Phone: (615) 936-7875
Location 107 Hill Center
Immunology Core
Michael Rock, Ph.D.
What we can do for you:
• Consultation on experimental and clinical trial design involving immune monitoring • Individual budget preparation • Processing and storage of samples (Peripheral Blood, Serum, Plasma etc.) • Multiplex cytokine assays (Cytometric Bead Arrays and Mesoscale Discovery) • Elispot Assays • Phenotypic analysis with flow cytometry • Multifunctional/Polychromatic flow cytometry (7-14 color) • Intracellular staining (cytokines, granzymes, etc.) • Cell proliferation assays • Tetramer/pentamer staining • Influenza HAI • Pertussis (PT) ELISA • Data analysis, management and reporting
The Immunology Core provides a wide-range of support and assays to assist investigators in their research with a primary interest in assessing cellular immune responses during clinical trials. We strive to support researchers with sample processing, storage, shipping, documentation, assay design, assay development and evaluation of immune responses. Our dedicated staff can provide consultation to investigators on the types of immune assays to choose for clinical trial monitoring and data interpretation. It is the goal of the core to monitor immune responses during clinical trials using the latest advances in technology and provide practical applications of this technology to evaluate immune responses. The Immunology Core has extensive experience in assay development and optimization, and will assist in the selection of appropriate assays during the protocol/developmental phase of a study or trial. A listing of assays can be found below; however, each study design may have unique features that require careful consideration, development and optimization prior to testing samples. Thus, specific assay conditions are not described in detail. • Consultation on experimental and clinical trial design involving immune monitoring • Individual written protocol and budget preparation • Processing and storage of samples from clinical trials (Peripheral Blood, Serum, Plasma etc.) • Multiplex cytokine 96-well plate based assays (Cytometric Bead Arrays and Mesoscale Discovery) • Elispot Assays • Phenotypic analysis with flow cytometry • Multifunctional/Polychromatic flow cytometry (7-14 color) • Intracellular staining (cytokines, granzymes, etc.) • Cell proliferation assays • Tetramer/pentamer staining • Influenza HAI • Pertussis (PT) ELISA • Cell-mediated immune response assay development • Data analysis, management and reporting • Generation and maintenance of viability and cell recovery data
Acknowledgment Text Immunology experiments were performed in the VUMC Immunology Core If you utilized a Starbrite grant (or any CTSA funding) to pay for your Core services please acknowledge this by using the following text: "Supported in part by Vanderbilt CTSA grant 5UL1 RR024975-03 from NCRR/NIH"
Contact Information Email: [email protected] Phone: 322-4494
Location Medical Center North Lab/Sample Drop-Off (cytokine analysis): T3316 MCN
Innovative Translational Research Shared Resource (ITR)
Director: Kimberly Brown Dahlman, PhD Laboratory Manager: Jamye O’Neal, BS
ITR Services House blood and tumor samples for clinical correlative studies Prepare blood for serum/plasma cytokine or lymphocyte analyses Isolate DNA and RNA from blood, tumor samples, and/or cell lines and design assays for (not
limited to): o SNaPShot genotyping o PCR and sequencing (design primers and analyze data) o Real‐time PCR (design primers and analyze data) o Next-generation sequencing o Microarray o Gene copy number
Custom studies (including pre‐clinical, western blotting, tissue culture, etc.)* *Subject to Advisory Board Review. Please contact Kimberly Dahlman for details. *Subject to Advisory Board Review. Please contact Kimberly Dahlman for details.
Mission: Advance the translation of basic and clinical research into improved patient therapies by facilitating discoveries and managing laboratory and clinical data exchange between researchers. General ITR Services: 1. Guide the initiation of Phase I and Phase II clinical correlative studies. 2. Manage the completion of Phase I and Phase II correlative studies utilizing Vanderbilt Shared
Resources or outside resources, where applicable: 3. Foster collaborations between clinicians and researchers to disseminate data from clinical
correlative studies and/or clinician‐initiated pre‐clinical studies. 4. Facilitate analyses of patient samples for research community and support collaborations with
clinical investigators.
Contact Information Website: http://www.vicc.org/research/shared/translational/ Email: [email protected] Phone: 615-936-0410
Acknowledgment Text The ITR is supported by the Vanderbilt-Ingram Cancer Center and the TJ Martell Foundation. We would also like to thank the ITR Advisory Board, Department of Cancer Biology, and Drs. Jeff Sosman and Madan Jagasia for support.
Location 722 Preston Research Building
Islet Procurement and Analysis Core Director: Marcela Brissova, PhD
Research Assistant: Anastasia Coldren
What we can do for you:
Pancreatic islet isolation from mice
Studies of hormone secretion by pancreatic islets
Islet RNA isolation
Help with experimental design/data analysis
Islet isolation training
Whole-slide scanning and analysis in bright field and fluorescence
Scheduling: E-mail [email protected]
Marcela Brissova Anastasia Coldren Wendell Nicholson Core Director Research Assistant Senior Research Specialist Phone: 615-936-1729 Phone: 615-936-2858 Phone: 615-936-1624
Contact Information Website: http://www.mc.vanderbilt.edu/diabetes/drtc/islet_procurement.php Email: [email protected]
[email protected] [email protected]
Phone: (615) 936-2858
Acknowledgment Text The Islet Procurement and Analysis Core is supported by the Vanderbilt Diabetes Research and Training Center (DK20593).
Location Medical Research Building IV (Langford) Room 8445C
Mass Spectrometry CoreCoreManager:WadeCalcuttPh.D.CoreDirector:DaveHacheyPh.D.
What we can do for you:
Areas for Mass Spectrometry analysis: Mass Spectrometers:
Qualitative and quantative analysis of drugs and metabolites
Nucleic Acids
Intact proteins (MS)
peptides (LC/MS/MS)
H/D exchange
Lipidomics
Accurate Mass determination
4x Thermo TSQ Quantums
Waters Synapt Q-TOF
2xThermo LTQ
LCQ Deca-XP
Trace DSQ GC/MS
Voyager DE-STR, MALDI TOF
For Training and Consultation please contact Wade Calcutt
We provide cost effective, state-of-the-art instrumentation to students, fellows, and faculty. Our facility is operated as an open-access core laboratory in which users are encouraged to run their own samples with the advice and assistance of Core personnel. Low cost service fees are charged at an hourly rate for instrument use.
Contact Information Website: http://www.mc.vanderbilt.edu/root/vumc.php?site=msrc/mass_spectrometry_core_lab Email: [email protected] Phone: (615) 343-8601
Acknowledgment Text Major Funding Sources - Center in Molecular Toxicology (5 P30 ES000267), Cancer Center Support Grant (5 P30 CA068485), Research Center for Pharmacology and Drug Toxicology (2 P50 GM015431), Molecular and Cellular Basis of Digestive Diseases (5 P30 DK058404)
Location Room 9126, MRB III
Molecular Cell Biology Resource Cores Kris Ellis, Core Manager
What we can do for you: The MCBR cores provides Vanderbilt researchers convenient access to reagents and instruments through:
A stockroom to shop for reagents 24/7 or order online with free delivery.
A DNA/RNA oligo and siRNA ordering service.
A primer design and optimization service for your PCR needs.
An instrument facility to assist with data collection, analysis, and documentation.
Training: Please see our friendly staff for instrument training or assistance. MCB Resource Core Catalog & Scheduling: https://cfuis.mc.vanderbilt.edu/login.cfm
Our stockroom carries a broad range of assays, kits, and reagents including DNA and RNA isolation kits, Western blot reagents, buffers, antibodies, enzymes, and much more (see catalog or request a special order). For rapid DNA/RNA oligo and siRNA ordering go to our website (http://thecore.vanderbilt.edu) to complete an order form. Our PCR primer design and optimization service is available to assist you in the development of PCR assays for your specific targets, saving you time and money. The instrument facility houses real-time PCR systems, gel/filter/film documentation equipment, various scanning and plate reading systems for absorbance, luminescence, fluorescence and radioisotopic detection.
Contact Information Website:http://thecore.vanderbilt.edu Email:[email protected] Phone: (615) 322-7238
Administered by the
Location Light Hall 902
Mouse Metabolic Phenotyping CenterCoreManager:FranTripp
CoreDirector:DavidWasserman,PhD
What we can do for you:
The MMPC is a comprehensive phenotyping center for mouse models of diabetes, obesity and related disorders.ers.
Tests for insulin resistance and glucose balance, heart and kidney function.
See a complete list of Vanderbilt University School of Medicine MMPC tests at (http://www.mc.vanderbilt.edu/root/vumc.php?site=mmpc)
For training or to schedule service, please email [email protected]
Metabolic Pathophysiology Core – Major procedures and tests: vein/artery cannulations, glucose and insulin clamps, glucose tolerance tests, tissue specific glucose/fatty acid uptake, calorimetry, exercise, gluconeogenesis/glycogenolysis, body composition, food consumption, optical imaging of gene expression/cellular events, isolation of pancreatic islets/insulin secretion. Cardiovascular Pathophysiology & Complications Core – Major tests: morphology and histology, echocardiography, electrocardiography, blood pressure, vascular morphology, myocardial infarcts, aortic banding, metabolic panel, glomerular filtration rate, telemetry, albumin/creatinine Hormone Assay and Analytical Resources Core – Major tests: plasma hormones, amino acids, lipids and lipoproteins, pathology and immunohistochemistry
Contact Information Website: http://www.mc.vanderbilt.edu/root/vumc.php?site=mmpc Email: [email protected] Phone: (615) 343-1065 OR (615) 322-0308
Acknowledgment Text The Mouse Metabolic Phenotyping Center is supported by NIH Grant DK59637
Location 843 Light Hall
Mouse Neurobehavioral Laboratory
Core Manager: John Allison Core Directors: Danny Winder and Gregg Stanwood
What we can do for you: The core has established assays for
• basic neurological examination • motor coordination • locomotor activity • anxiety • learning and memory • cognition • sensorimotor gating • social behaviors • drug abuse • depression-related behaviors.
For training and scheduling, please email: [email protected]
The Murine Neurobehavioral Lab (MNL) is a shared resource, available for all researchers with appointments in the Vanderbilt University Medical Center. The MNL is supported by the Vanderbilt Brain Institute, the Kennedy Center, and by fees assessed for usage. Non-VUMC personnel may also use the facility. Resources include open field activity chambers, acoustic startle chambers, operant conditioning chambers, drug self-administration chambers, a Morris watermaze, automated elevated plus mazes, Barnes maze, T-maze, 8-arm radial maze, and items necessary for doing an Irwin screen (e.g., rotorod). Surgical and dissection area are also available.
Contact Information Website: www.vandymouse.org Email: [email protected] Phone: (615) 322-0794
Location AA9100, MCN
Acknowledgment Text
Experiments/Data analysis/presentation [include what you use] were performed in part through the use of the Murine Neurobehavior Core lab at the Vanderbilt University Medical Center.
Neurochemistry Core LabCoreManager:RayJohnsonCoreDirector:ArielDeutch
What we can do for you:
Tissue determinations of:
o Biogenic Amines
o Amino Acids
o Acetylcholine/Choline
Whole blood determinations of Serotonin
Plasma catecholamine determinations
Instruction/Consultation on the use of HPLC instrumentation
The Neurochemistry Core offers high sensitivity and fast throughput assays for monoamines and amino acid neurotransmitters and their metabolites. Using HPLC separation followed by fluorescent and/or electrochemical detection, the core assays can reliably detect femtomole to picomole quantities of amino acid and them major amine neurotransmitters (NE, DA, 5HT, ACh) and their metabolites in microdissected brain (or peripheral organ) samples and from in vivo microdialysis samples. Custom development of assays is available (with investigator participation required). Sample are returned within two weeks of submission (often more quickly), with data including the concentration (expressed as ng or fmol/mg protein) for each sample.
Contact Information Email: [email protected] Phone: (615) 322-4496 OR (615) 417-2346
Acknowledgment Text HPLC determinations were performed by the CMN/KC Neurochemistry Core Lab at Vanderbilt University. The CMN/KC Neurochemistry Core Lab is supported by Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt Conte Center for Neuroscience Research and The Vanderbilt Center for Molecular Neuroscience.
Location 6141 MRB III 6143 MRB III
Proteomics Laboratory Shared Resource Director:KevinL.Schey,PhD
AssociateDirectors:W.HayesMcDonald,Ph.D.;KristieL.Rose,Ph.D.
What we can do for you: We specialize in a wide variety of protein/peptide separations and mass spectrometry to support an array of proteomics technologies, including:
Mass spectrometry (MS) based protein identification from simple or complex samples in solution or resolved by SDS-PAGE (coomassie-blue stained)
Global quantitative protein expression analysis from peptide digests analyzed by MS (iTRAQ, SILAC, and spectral counting)
Post-translational modification mapping and characterization by high-resolution MS: o Phosphorylation o Acetylation o Ubiquitination
Targeted absolute and relative protein quantification by selected- and multiple-
reaction monitoring MS
Stable domain/structure analysis
Pre-consultation on experimental design for all projects
Contact Information http://www.mc.vanderbilt.edu/root/vumc.php?site=msrc/proteomics_core
Kevin Schey, Director [email protected] 936-6861 Kristie Rose [email protected] 343-1568
Hayes McDonald [email protected] 343‐0512
Location 9110 MRB III
We are a limited-access facility and perform all proteomic analyses with our staff. We work closely with all users from experimental design through data analysis. All projects begin with a
pre-consultation with one of the Associate Directors.
ESI-ion trap (ThermoFisher) (3x) LTQ Q Exactive Orbitrap ETD-enabled LTQ-Orbitrap Velos Eksigent and Waters nanoflow LC systems
Triple quadruple (ThermoFisher) TSQ Vantage with Waters NanoAcquity LC
MALDI-TOF/TOF (Applied Biosystems) Voyager 4700 system
Major Instrumentation
Rat Neurobehavioral Laboratory
Core Manager: Randy Barrett
What we can do for you:
The core has established assays for:
motor coordination locomotor activity anxiety learning and memory cognition sensorimotor gating social behaviors drug abuse depression-related behaviors surgery
For training and scheduling, please email: [email protected]
The Rat Neurobehavioral Lab (MNL) is a shared resource, available for all researchers with appointments in the Vanderbilt University Medical Center. The RNL is supported by the Vanderbilt Brain Institute and by fees assessed for usage. Non-VUMC personnel may also use the facility. Resources include open field activity chambers, acoustic startle chambers, operant conditioning chambers, drug self-administration chambers, a Morris watermaze, elevated plus maze, T-maze, novel object arena, 5-choice serial reaction time chambers, conditioned place preference chambers and locomotor activity chambers. Surgical and dissection areas are also available.
Contact Information Website: http://medschool.mc.vanderbilt.edu/rat_core/ Phone: (615) 343-4300
Location AA9100, MCN
Acknowledgment Text
Experiments/Data analysis/presentation [include what you use] were performed in part through the use of the Rat Neurobehavior Core lab at the Vanderbilt University Medical Center.
Vanderbilt Sleep Research CoreCoreManager:LukeGoodpaster,BA,RPSGT,RST
CoreDirector:BethMalow,MD,MS
What we can do for you:
All services are provided for both adult and pediatric populations:
1. Polysomnography (Sleep Studies)
2. Polysomnography Interpretation
3. Centralized Sleep Data Management Site
4. Electroencephalography (EEG)
5. Actigraphy
6. Portable Sleep Testing
It is estimated that humans sleep nearly one third of their lives. Yet, the variable of sleep is often overlooked. The Vanderbilt Sleep Research Core was developed to facilitate interdisciplinary research of sleep (adult and pediatrics, neurology, pulmonary, psychiatry) and its relationships with health and waking function. We offer a variety of services that give investigators objective measurements in easy to use formats.
1. Polysomnography (PSG) - Gold standard in objective sleep testing, measures brain waves, eye movements, muscle tone, heart rhythms, oxygen, respiratory effort, airflow, etc. Trial-specific measurement tools can be also used in conjunction with the standard PSG.
2. Polysomnography Interpretation - PSG data must be interpreted in a reliable and consistent manner to allow for findings to be reproduced. This service allows for investigators that have little or no knowledge of interpreting PSG data to be able obtain data in a useful manner.
3. Centralized Sleep Data Management Site- Data collected in multicenter projects can be interpreted here at one centralized location to maintain consistently across all sites. Interaction between sites is essential for this process to work properly. Quality Assurance measures are used to aid all sites in data collection.
4. Electroencephalography (EEG) - 21 lead full EEG commonly used to measure electrical activity of the brain. This service can be used in projects that have no relationship to sleep.
5. Actigraphy - Small non-intrusive watch like device used to measure sleep-wake patterns across long periods of time.
6. Portable Sleep Testing - Can be performed in settings outside of the lab, but lacks the level of reliability of the standard in lab PSG.
Contact Information Email: [email protected] Phone: (615) 343-2532
Acknowledgment Text The Vanderbilt Sleep Research Core is administered by the Vanderbilt Department of Neurology. We would also like to thank Vanderbilt Clinical Research Center and Dr. Michael DeBaun for their support.
Location AA3223, MCN
Tissue Profiling and Imaging Core Core Manager: Erin Seeley and Michelle Reyzer
Core Director: Richard Caprioli
What we can do for you:
Sample preparation for mass spectral analysis of tissue sections
Imaging mass spectrometry of proteins, peptides, lipids, and drugs/metabolites
Histology directed mass spectral profiling of frozen and FFPE tissue
Imaging mass spectrometry of tissue microarrays
Data processing of images and classification algorithm for biomarker discovery
The tissue profiling and imaging core provides expertise in tissue imaging and histology directed tissue profiling by MALDI MS whereby thin sections of tissue are analyzed for the localization of biomolecules. The imaging process produces a picture of the two dimensional distribution of molecules across the tissue section. Histology directed profiling targets discrete areas for analysis using a stained serial section as a guide and is conducive to high throughput analysis. Target analytes include proteins, peptides, lipid, and drugs/metabolites.
Contact Information Website: http://www.mc.vanderbilt.edu/root/vumc.php?site=msrc/tissuecore Email: [email protected] Phone: (615) 343-2718 Acknowledgment Text Tissue profiling and imaging studies are supported by Vanderbilt Ingram Cancer Center Core Support Grant 3P30 CA068485-14 and the National Resource for Imaging Mass Spectrometry at Vanderbilt University supported by NIH grant 5P41 RR031461-02.
Location MRB III U9220
Transgenic Mouse/Embryonic Stem Cell Shared Resource Core Manager: Jennifer Skelton
Core Director: Mark Magnuson, Doug Mortlock, Susan Mijka
What we can do for you:
Pronuclear DNA Microinjections
ES Cell Microinjections
Rederivations/Assisted Reproduction Technologies
Embryo Cryopreservation
Sperm Cryopreservation
Cryostorage
Gene Targeting
Recombinase-Mediated Cassette Exchange (RMCE)
Karyotyping
BAC Recombineering
Southern Blot Hybridization
Scientific Consultation
The Transgenic Mouse/ES Cell Shared Resource has been in existence since 1993 and provides a wide array of essential services for the generation, maintenance, and long-term storage of germline-altered mice. Recently, we have expanded our service offerings to include RMCE, BAC recombineering and Southern blot hybridizations. In addition to striving to provide timely and reliable service, we also provide expert scientific consultation to facilitate the development of new mouse models.
Contact Information Website: http://labnodes.vanderbilt.edu/tmescsr Email: [email protected] Phone: (615) 936-3454 or (615) 936-2052
Acknowledgment Text Use of this Resource should be acknowledged in all publications. The Cancer Center Support Grant (CA68485), the Vanderbilt Diabetes Research and Training Center (DK20593), the Center for Molecular Neuroscience, and/or the Center for Stem Cell Biology should be cited unless prohibited by the editorial policy of the journal.
Location 9410 MRB IV 2213 Garland Avenue Nashville, TN 37232
Translational Pathology Shared ResourceCoreManager:MeganM.CookCoreDirector:Dr.MaryZutter
What we can do for you:
Collection and access to consented and de-identified human tissue specimens Comprehensive, diagnostic, necropsy and comparative pathology services for
animal model systems with specific expertise in mouse models Research histology including immunohistochemistry, immunofluorescence, laser
capture microdissection and tissue microarray preparation
For training, please email: [email protected]
The Translational Pathology Shared Resource (TPSR) represents both a consolidation and expansion of the Human Tissue Acquisition and Pathology Shared Resource (HTAP) and the Immunohistochemistry Core, as well as, the addition of Comparative Pathology Services and expertise. The research histology service for human and animal based tissue assays includes routine histology, special stains and sectioning requests, immunohistochemistry, immunofluorescence, validation of novel antibodies, laser capture microdissection, and tissue microarray preparation. The new comparative pathology section offers pathology phenotyping of mouse models and diagnostic services such as hematology, clinical chemistry, cytology, microbiology, parasitology, necropsy, and training on tissue handling techniques. The research histology and comparative pathology services are located in a new 3000 square foot renovated facility located in Medical Center North. Human tissues are collected prospectively from routine surgical resections and autopsies for use by investigators in basic, translational and clinical research studies. Only remnant tissue samples not needed for diagnostic purposes are collected. These tissues are available fresh, snap forzen, or in a variety of fixatives as requested by the investigator. Normal, neoplastic, and other diseased tissues are available for study.
Contact Information Website: http://www.mc.vanderbilt.edu/root/vumc.php?site=tpsr Email: Tissue Acquisition ‐ [email protected] Research Histology ‐ TPSR‐[email protected] Comparative Pathology ‐ TPSR‐[email protected] Phone: (615) 322-3667
Acknowledgment Text The Translational Pathology Shared Resource is supported by funds from Vanderbilt University School of Medicine, VICC, and the Division of Animal Care. Please acknowledge use of this core in any publications resulting from services performed by this facility. Cancer researchers should list Cancer Center Support Grant 5P30 CA068485. Diabetes researchers should list Mouse Metabolic & Phenotyping Center 5U24 DK059637.
Location MCN, 1st Floor, S 1310
VANGARD Core Manager: Lynne Berry
Core Director: Yu Shyr
What we can do for you:
Genotying data: QC, SNP calls, association analysis NGS data (RNAseq, DNAseq, ChIPseq, miRNAseq): as appropriate to each technology:
QC
alignment
SNP calls
expression quantification and comparison
structural variant analysis
gene-level analysis
functional/pathway analysis Other genomics analysis Scheduling: [email protected] VANGARD offers data processing, quality control (QC), and downstream analysis for all major genomics technologies, including array-based genotyping (GWAS and non-GWAS platforms), RNA-seq, DNA-seq (whole genome, exome, or targeted panel), ChIP-seq, and miRNA-seq. Services are available for both eukaryotic and prokaryotic genome analysis. Standard services are priced per service module, with an hourly rate also available for service requests that do not fall into an established module.
Contact Information Email: [email protected] Phone: (615) 936-2502 OR (615) 936-2572
Acknowledgment Text We wish to acknowledge the VANGARD core for services provided for genomic data analysis.
Location 571 PRB
VANTAGE: (Vanderbilt Technologies for Advanced Genomics) Scientific Director: James Crowe, MD
Associate Director for Genomics: Jeffrey Smith, MD, PhD Technical Director, Sequencing: Travis Clark, PhD
Technical Director, HT Genotyping and Expression: Holli Dilks, PhD Manager, Bio-banking and Genotyping: Cara Sutcliffe, MS
What we can do for you:
DNA Extraction from blood, buccal cells, or various tissues
Biological Sample Banking (DNA, whole blood, blood spots, etc.)
Nucleic acid quality control
Microarray expression analysis
Genotyping using Taqman, Sequenom, Affymetrix, and Illumina Chemistries
Sanger Sequencing
Next-generation sequencing
For training or for further information: please go to vantage.vanderbilt.edu
Scheduling: Reservations for some instruments are available online through CORES. Drop-ins welcome for extraction samples or project consultation.
VANTAGE provides services in human DNA extraction, sample banking, genotyping, gene expression, sequencing, and other services that support molecular genetics & genomic studies. Most DNA extractions can be performed with one of our Autopure robots, which use PureGene reagents & bar-coding for efficient sample handling. We offer custom genotyping services with our ABI 7900 platform for TaqMan Allelic Discrimination assays, the Sequenom MassARRAY, Affymetrix cartridge arrays, the Illumina BeadXpress, the Illumina iScan and HiScan platforms. Sanger sequencing is supported by our two ABI 3730 capillary array sequencers and Next-Generation Sequencing is supported by two Illumina HiSeq2500’s and two Illumina MiSeq’s.
Contact Information Website – vantage.vanderbilt.edu Email – Please fill out the “Contact Us” form on the website to direct your message to the appropriate manager. Phone – 615-936-2744 (Cara), 615-343-2607 (Holli), 615-936-3003 (Travis)
Acknowledgment Text VANTAGE is supported by the Vanderbilt Ingram Cancer Center (P30 CA68485), the Vanderbilt Vision Center (P30 EY08126), and NIH/NCRR (G20 RR030956).
Location T-0102 MCN and S-0102 MCN
VICB Chemical Synthesis Core Core Manager: Padma Portonovo Core Director: Gary Sulikowski
What we can do for you:
Synthesis of Single Compounds (small and large quantity)
Small Molecule Probes and Drug Candidates
Small Compound Libraries (MedChem)
Heterocycles, Fluorescent Probes, Single Enantiomers (we will consider delivery of any organic compound aside from macromolecules)
Scheduling: see http://www.vanderbilt.edu/syncore/
The VICB Chemical Synthesis Core provides a full range of organic synthesis and medicinal chemistry services including:
Synthesis of literature-cited and patented compounds. Design and synthesis of unknown compounds. Hit validation and optimization. Structure-activity relationship analysis. Large-scale synthesis. Compound purification. Training services in the use of compound purification equipment (HPLC). Walkup use of purification equipment (HPLC).
Contact Information Website: http://www.vanderbilt.edu/syncore/ Email: [email protected] Phone: 615-343-0869
Acknowledgment Text If the core lab provides compounds that are used in your publication please use this acknowledgement: “Compound X” was provided by the Vanderbilt Institute of Chemical Biology, Chemical Synthesis Core, Vanderbilt University, Nashville, TN 37232
Location 12410-D MRB-IV (LG) Vanderbilt University 2213 Garland Avenue
VICB High Throughput Screening Core Facility Core Manager: Lisa Wright
Core Director: Paige Vinson
What we can do for you:
Assay Design and Validation
High-Throughput Screening
Data Analysis
Training for Walkup Use of Plate Readers
Compound Distribution
For training or scheduling: [email protected]
http://www.vanderbilt.edu/hts
The goal of the HTS CORE is to provide a wide variety of screening-based services to the Vanderbilt research community. From training users for self-service plate reading and compound distribution, to full high-throughput drug screens, the CORE provides all necessary resources and staff. The HTS facility possesses a variety of plate readers and liquid handling equipment to fit a diverse set of scientific needs. Additionally, all Vanderbilt researchers are allowed to take advantage of the compound libraries stored in our Universal Store Automated Sample Freezer. With these resources available in the HTS facility, we are positioned to guide researchers through the early part of the drug discovery process from assay or project conception to lead identification. At the HTS facility, we serve the basic research needs of scientific investigators by providing walk-up access to state-of-the-art instrumentation, distribution of compound libraries, and informatics solutions.
Contact Information Website: http://www.vanderbilt.edu/hts Email: [email protected] Phone: (615) 936-7098
Acknowledgment Text The High Throughput Screening Core Facility is part of the Vanderbilt Institute of Chemical Biology.
Location 824 Robinson Research Building
VICB Vanderbilt Antibody and Protein Resource (VAPR) Scientific Director: Al Reynolds
Managing Director: Rob Carnahan
What we can do for you:
Custom Monoclonal Antibody Development Large Scale Generation and Purification of Monoclonal Antibodies Custom Polyclonal Antibody Development Affinity Purification of Polyclonal Antibodies Bacterial Recombinant Protein Production and Purification Baculovirus Recombinant Protein Production and Purification Mammalian Recombinant Protein Production and Purification Mammalian Stable Cell Line Development Optimization Kinetic and Association Analyses for Protein/Protein & Protein/Small molecules Antibody Repository for many common and affinity tag antibodies (GFP, Myc, HA,
GST, tubulin, etc.) Enzyme repository for commonly used items (taq polymerase, high fidelity
polymerase, proteases, etc.)
Scheduling and Project Initiation: Please submit a project request form at http://www.vanderbilt.edu/vapr
Contact Information Website - www.vanderbilt.edu/vapr Email - [email protected] Phone - 615-936-3092 / 615-322-5623
Acknowledgment Text Antibodies/Proteins were produced/purified by the Vanderbilt Antibody and Protein Resource. The Vanderbilt Antibody and Protein Resource is supported by the Vanderbilt Institute of Chemical Biology and the Vanderbilt Ingram Cancer Center (P30 CA68485).
Location Preston Research Building 892 2220 Pierce Ave
The central VAPR mission is to make state-of-the-art antibody and recombinant protein technologies cost effective and readily available to Vanderbilt Investigators. The VAPR provides reagents, equipment, protocols, and expert assistance in all aspects of production, purification, detection, and characterization. In addition, a wide variety of specialized services related to antibody assays and usage are offered at cost with rapid turnaround. Our large-scale recombinant protein production and purification include both bacterial and mammalian cells. We have also recently added biomolecular interaction analyses with the addition of the Forte Bio Octet Red instrument.
VIIBRE Automated Biosystems Core (ABC) Core Manager: Vanessa Allwardt
Core Director: John P.Wikswo, Ph.D.
What we can do for you:
PerkinElmer Opera QEHS - Ultra-Highspeed Confocal Screening Microscope Approx. 125,000 images per day (up to 400 images/min) 4 laser sources (405, 488, 561, 640nm) + UV/Vis (350-410nm), brightfield TLED 4 CCD cameras (1.3 MP, 12-bit), wide range of fluorescent filter combinations 10x, 20x, 40x air objectives; 20x, 40x water-immersion objectives
PerkinElmer Columbus Imaging Software Comprehensive and intuitive high-volume image analysis software with custom analysis scripts and powerful machine-learning capabilities for complete in-depth wellplate analysis in minutes. PerkinElmer Volocity 3D Image Analysis Software Measure, analyze, and relate your images and data in 3D. Capabilities include automated 3D cell tracking, colocalization, morphological analysis, FRAP, FRET, 3D movies, and more. Analyze multiple samples in batch. Example Applications: Toxicity and survival, systems biology, RNAi screening, stem cell screening, phenotypic assays, drug discovery and much more! Training and Scheduling: Please email [email protected]
The ABC is a high-content screening/imaging resource utilizing the PerkinElmer Opera, an ultra-highspeed confocal screening microscope suitable for wellplate use, and PerkinElmer Columbus Imaging Software for high-volume image data analysis.
Contact Information Website: http://www.vanderbilt.edu/abc Email: [email protected] Phone: (615) 343-4124
Acknowledgment Text This core is supported in part by NIH Grant 1S10RR027485-01, VUMC, and the Vanderbilt Institute for Integrative Biosystems Research and Education (VIIBRE).
Location Stevenson Center - 6123B Stevenson Center - 6823
VIIBRE Microfabrication Core Core Manager: David Schaffer Core Director: John Wikswo
What we can do for you:
Microfabrication Photolithography
Mask design & layout Microfluidic networks
Microfluidic control systems Custom implantable devices
Biological habitats Microbioreactors
Machining
For training, please email: [email protected]
Scheduling & information: http://www.vanderbilt.edu/mfc
The VIIBRE Microfabrication Core offers facilities and expertise for the design, manufacture, and implementation of micro- and small-scale electronic, mechanical and fluidic devices. Typical products include fluidic networks,pumps and valves, arrays of microfabricated traps for cellular study, implantable devices for in vivo imaging, liquid and gas control systems, biological habitats, environments and microbioreactors, and more.
Contact Information Website: http://www.vanderbilt.edu/mfc Email: [email protected] Phone: (615) 343-7108 x1
Acknowledgment Text Vanderbilt Institute for Integrative Biosystems Research & Education (VIIBRE)
Location 6800 Stevenson Center
VUIIS Center for Small Animal Imaging Director: Mark D. Does
Manager: Jarrod M. True
What we can do for you:
In vivo and ex vivo imaging of small animals and tissue samples via:
Magnetic resonance imaging
Ultrasound
X-ray/X-ray CT
Positron emission (PET) and single photon emission tomography (SPECT)
Digital Autoradiography
Bioluminescence/fluorescence Imaging
We provide training for users on ultrasound and optical imaging, and provide expert instrument operators for other modalities. We also provide expert support/training for data/image analysis
The Center for Small Animal Imaging (CSAI) is dedicated to research studies of small animals for a variety of applications. The Center provides access to high field magnetic resonance imaging and spectroscopy (4.7T, 7T and 9.4T for small animals: 4.7T for awake non-human primates, and 0.5T for small samples), high resolution X-ray computed tomography (microCT), digital radiography (Faxitron), nuclear imaging techniques (high resolution microPET, nanoSPECT, and gamma ray imaging), high resolution ultrasound, and optical (in vivo bioluminescence and fluorescence) imaging. The center also has a cryomicrotome to section whole animals to allow registration of in vivo imaging with histology and proteomic data. The CSAI is staffed with imaging and animal technologists and is supported by instrumentation engineers and a computer systems manager. VUIIS faculty and trainees are active in developing novel methods of imaging to obtain new types of information as well as in applying current methods to study a wide range of biomedical questions.
Contact Information Website: http://vuiis.vanderbilt.edu/resources/CSAI.php Email: [email protected] Phone: 322-8352
Location Medical Center North AA-2105
VUIIS Center for Human Imaging Director: Seth Smith
Manager: Brian Welch
What we can do for you:
• Structural and functional MR Imaging and Spectroscopy at 3 and 7 Tesla
• MRI/MRS protocol development support
• fMRI experimental design support
• Quantitative imaging
• Subject preparation and pre-/post-testing facilities
• Structural and functional image analysis
• Training on image analysis techniques and tools
The Center for Human Imaging, located on the ground floor of the Vanderbilt University Institute of Imaging Science (VUIIS), as well as in VUH, provides facilities and technical support for structural, metabolic and functional imaging of human subjects. Facilities include two state-of-the-art 3T MR scanners capable of imaging and multi-nuclear spectroscopy, and an advanced 7T human scanner. Other modalities include near infrared optical topography (NIROT), and event-related potential (ERP) electroencephalography. VUIIS faculty also have access to extensive clinical imaging resources including PET-CT. Ancillary equipment is available to provide continuous physiological monitoring of subjects, and to generate and deliver stimuli and monitor and record responses during studies of brain function. The Center for Human Imaging expert staff is available for data acquisition and analysis support and training. An extensive suite of image analysis software and workstations are available for users.
Contact Information Website: http://www.vuiis.vanderbilt.edu/resources/human.php Email: [email protected] Phone: 322-6211
Location Medical Center North AA-0117
VUIIS Radiochemistry Core Research Program Director: H. Charles Manning, Ph.D.
Technical Director: Michael L. Nickels, Ph.D.
What we can do for you: Development of new and established radiopharmaceuticals for human and animal investigations
Radiolabelling of precursors and intermediates for imaging studies using
[18F]F- in aqueous solution, [11C]CO2 gas, [11C]CH3I methyl iodide, and [64Cu]CuCl2 in dilute HCl Commercial Products and Pharmacy Items
[18F]FDG (2-fluoro-2-deoxyglucose; glucose metabolism), [18F]fluoride (bone, fluoride metabolism), [99mTc]pertechnetate, [99mTc]Tc-MDP, [99mTc]Tc-HMPAO, [111In]In-DTPA
Research Radiopharmaceuticals Radiopharmaceuticals for human or animal imaging: [18F]fallypride (dopamine D2/D3), [18F]FECNT (dopamine transporter), [18F]FLT (cell proliferation, nucleoside metabolism), [18F]setoperone (serotonin 5-HT2a receptor), [18F]FES (estrogen receptor), [18F]PBR06 (translocator protein). Radiotracers for animal/in vitro studies: [18F]FP-DTBZ (vesicular monoamine transporter), [18F]FMISO (hypoxia, tumor imaging), [18F]DPA-714 (translocator protein), [64Cu]copper-ATSM (cell hypoxia, tumor imaging), [11C]acetate (citric acid cycle, acetate metabolism), [18F]fluorocholine (choline metabolism), [18F]TSPO ligands (various), [18F]SFB (peptide labeling agent)
Radiotracers in Development [11C]choline, [18F]folate, [18F]fluoro-L-tryptophan, [18F]VADFMK, [18F]glutamine, [18F]glutamate
Radiotracer Drug Discovery Radiolabeled ligands for the peripheral benzodiazepine receptor (PBR), radioligands for amyloid protein, agonist radioligands for the dopamine D2 receptor, COX-2 imaging agents.
The radiochemistry facility is housed in the PET Center in the Robinson Research Building and is well equipped for radiochemical preparations that use common radionuclides. The core is equipped with a GE 130 A PETtrace negative-ion cyclotron with targets and ancillary equipment optimized for generating 18F, 11C, 13N, and related radionuclides. Adjacent laboratories utilize two Von Gahlen hot cells with CRL manipulators, two radiation shielding hot cells with Tru-Motion manipulators, and two "dual mini-cells" housing two GE TRACERlab FX F-N fluorination modules, two Bioscan Coincidence Reaction Modules, and a GE TRACERlab FX C Pro gas phase 11C methyl iodide/methylation module. Three radiochemical hoods are designated for lower-level work with short-lived gamma-emitting radionuclides other than iodine. Additionally, a dedicated radioiodination hood, equipped with activated carbon filters, is located in a separate laboratory for 123I and 125I manipulations. A total of four independent Hitachi High Technologies HPLC systems with UV (conventional and UV-Vis) and radiometric detectors are in use for daily production and research. In addition to the HPLC systems, the core possesses two Bioscan radio-TLC scanners, a shielded Germfree biological safety cabinet, four microwave acceleration units, an Advion NanoTek microfluidic reaction module, and a Varian gas chromatograph. Through careful allocation of the resources at hand, we are capable of a rapidly steering a novel imaging agent through the winding process of concept to production. A second laboratory, with independent resources, is located in F1200 in MCN and is dedicated to the labeling of gamma ray emitters for SPECT imaging.
Contact Information Website: http://vuiis.vanderbilt.edu/resources/chemistry.php Email: [email protected] Phone: 322-3793
Location Robinson Research Suite 1200
Vanderbilt Zebrafish Core Facility – ZCORE Core Manager: Amanda Porterfield, M.S. Scientific Director: Ela W. Knapik, M.D.
Zebrafish is an excellent system for fast and inexpensive evaluation of gene function. In addition to being a staple developmental biology model system, zebrafish are also uniquely amendable to in vivo chemical and genetic screens, and they are commonly used for establishing animal models of human diseases. ZCORE is a 2,600 square foot aquatic facility with capacity for 90,000 fish, including a dedicated nursery room and two large separate systems for adult animals. Water is tightly controlled by a life-support system and a custom software interface. A dedicated tank washing facility and food preparation rooms are included. Instruments for embryo microinjection and fluorescent microscopy are also available on-site.
The ZCORE mission is to provide VUMC scientists with a direct access to the zebrafish model system in the form of:
• Aquaculture and husbandry of the zebrafish colony; • Embryo production; • Adult wild type lines; • Use of egg injection setup; • Use of Fluorescence Dissecting Microscope and Imaging setup
Training: Provided on site for registered users.
Contact Information Email: [email protected] Phone: 322-7569
Location ZCORE: Light Hall 109