research shared resources user handbook
TRANSCRIPT
VANDERBILT UNIVERSITY MEDICAL CENTER
RESEARCH SHARED RESOURCES USER HANDBOOK
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.
Location: Hill Center Suite 201
Advanced Computing Center for Research & Education (ACCRE)
Steering Committee: Dave Piston, VUMC; Ron Schrimpf, VUSE; Paul Sheldon, A&S
Computing Cluster: Carie Lee Kennedy; Storage Development: Alan Tackett
What we can do for you: Research Computing Cluster
Disk Storage
Tape Backup Service
Data Storage and Tape Archive Services to be added
Training: http://www.accre.vanderbilt.edu/education-outreach/training/index.php
Scheduling: Online job submissions for approved cluster users. New account requests at http://www.accre.vanderbilt.edu/support/contact/request_account.php
Contact Information Website: www.accre.vanderbilt.edu Email: [email protected]
Acknowledgment Text This work was conducted in part using the resources of the Advanced ComputinCenter for Research and Education at Vanderbilt University, Nashville, TN.
Atherosclerosis Subcore Core manager: Vladimir Babaev
What we can do for you:
We provide investigators with high quality, low cost and efficient analysis that facilitate research in atherosclerosis and lipoprotein metabolism
of
Training: Please call us (phone 61161 or 61673) to schedule the training
Scheduling: Our service may be requested or scheduled in direct contact (room 312 PRB) or by the phone (61161 or 61673).
We provide following services: 1. Mouse tissue collection 2. Atherosclerosis assessment and plaque analyses including quantification
of the extent of atherosclerotic lesions in the proximal aorta and in pinned out aorta en face, plasma lipids and lipoprotein distribution
3. Bone marrow transplantation to generate chimeric mice with different hematopoietic cells
4. Immunostaining to analyze atherosclerotic lesion composition 5. Laser capture microdissection to examine gene expression profiles in
atherosclerotic lesions
Contact Information Email: [email protected] Phone: 615-9361161
Acknowledgment Text This work was supported by National Institutes of Health grants DK59637 (LipidLipoprotein and Atherosclerosis Core of the Vanderbilt Mouse Metabolic PhenotypCenters).
Location Pierce Research Building Room 312
Cell Culture Core Scott Wright, Core Manager
What we can do for you:
Invitrogen media, Sera and supplements
Custom made tissue culture media and salt solutions
Agar plates and Competent Cells
The Cell Culture Core has many tissue culture items from Invitrogen in stock, and can order anything that is needed at discounted prices. Custom made media as well as agar plates and competent cells are always available. Free delivery. Contact Scott by email if you have any questions.
Contact Information Email: [email protected] Phone: 322-7608
Location Light Hall, 838
CFAR Immunopathogenesis Core Director: Spyros Kalams, M.D.
Manager: Louise Barnett
Contact Information Website - http://www.mc.vanderbilt.edu/cfar Email – [email protected] Phone – 615-343-5929/615-343-2864
Location 1161 21st Ave South Medical Center North A-2100
Acknowledgment Text “Flow cytometric cell acquisition or sorting was performed by the Vanderbilt-Meharry Center for AIDS Research (CFAR) Immunopathogenesis Core, an NIH funded program (P30 AI 54999).”
CFAR Immunopathogenesis Core houses a cell sorter and laser confocal microscope in a BSL3 facility, allowing for the study of biohazardous or infectious samples.
The BD FACS Aria IIu is a three laser (407,488,633) cytometer capable of eleven color fluorescence analysis and four-way sterile sorting for bulk collection of purified cell populations or single cell deposition for subcloning. The Perkin Elmer LCI is a three laser (488,567,633) fluorescent inverted confocal microscope with an environmental chamber for live cell imaging.
Instruments:
Becton Dickinson FACS Aria IIu Flow Cytometer
Perkin Elmer LCI Confocal Microscope
RoboSep Automated Cell Separator
Scheduling instrument time: Contact Louise Barnett at [email protected]
or call 343-5929.
Center for Human Genetics Research: Genetic Studies Ascertainment Core (GSAC)
Director: Holli Hutcheson Dilks, Ph.D. Project Manager: Kelly Taylor, MS, CGC
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
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. Currently, we work on genetic studies related to autism-spectrum disorders, age-related macular degeneration, diabetic retinopathy, glaucoma, epilepsy, Alzheimer disease, dementia, and Parkinson disease. We also work on projects involving various diseases in the Amish. To schedule a consultation, please contact a GSAC Manager or the GSAC Director.
Contact Information Website – http://chgr.mc.vanderbilt.edu/page/genetics-studies-ascertainment-core. Email – [email protected] OR [email protected]
Location 1207 17th Avenue South, Suite 100
CMN/KC Neurochemistry Core Lab Director: Ariel Deutch
Manager: Ray Johnson
What we can do for you:
Tissue determinations of Biogenic Amines, Amino Acids, 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 Website – www.vandyneurocores.org Email – [email protected] Phone - 615 322 4496
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 Building MRB III Room(s) 6141 - 6143
Computational Genomics Core CHGR Cores Director: Holli Hutcheson Dilks, Ph.D.
Core Director: Marylyn Ritchie
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 the information technology and data analysis 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 as it is generated by the DNA Resources Core or by individual investigators. Expertise in family based, case/control, GWAS (genome-wide association study), linkage, segregation, 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 - 615-343-8618
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 519 Light Hall
Clinical Research Center Core Lab Angie Sneed, Core Manager
What we can do for you:
The following analyses are currently available HPLC and ELISA Laboratory DNA Extraction (B) Catecholamine (P, U) Total Nitrogen (U) Cortisol (Sal) Nt-proBNP (P) Melatonin (Sal) 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.
Contact Information www.mc.vanderbilt.edu/crc [email protected] 615-343-3646
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 RR024975 from NCRR/NIH"
Location Medical Center North A-3219
CSB Biophysical Instrumentation Core Director: Walter Chazin Manager: Laura Mizoue
What we can do for you:
Jasco J-810 Circular dichroism spectropolarimeter
MicroCal VP-DSC Differential scanning calorimeter
Fluoromax-3 Steady-state fluorometer equipped with polarizers
MicroCal VP-ITC Isothermal titration calorimeter
We provide:
New user training
Unassisted access to instruments upon completion of training
Scheduling: User walk-up
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 http://structbio.vanderbilt.edu/wetlab/instrumentation.php [email protected] 615-936-2253
Acknowledgment Text “CD/Fluorometry/Calorimetry experiments were performed in the Vanderbilt Biophysical Instrumentation Core which is supported by the Vanderbilt Center for Structural Biology.”
Location MRBIII Rooms 5141, 5147
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
Division of Animal Care Core Manager- Michele Fritts, BBA/Director- Dr. Jeanne Wallace, DVM, DACLAM
What we can do for you:
Animal Procurement
Animal Husbandry
Animal Healthcare
Animal Transfers and Shipping
Training: https://www.vacup.us/dac/training-sops
The Division of Animal Care (DAC) is the service core of the Office of Research that provides
procurement, husbandry, and healthcare for experimental animals, as well as
scientific/technical support for VU researchers.
Our mission is to provide humane animal care that meets the highest national standards
supporting knowledge and discovery through research. To that end, the DAC endeavors to
provide excellent animal care and customer service in support of Vanderbilt’s research and
teaching programs.
Contact Information www.vacup.us 615-322-2231
Location Medical Center North AA-6206
DNA Resources Core Director: Holli Hutcheson Dilks, PhD Manager: Cara Ballard Sutcliffe, MS
What we can do for you:
DNA Extraction from blood, buccal cells, or various tissues
Genotyping using Taqman, Sequenom, and Illumina Chemistries
Specialized genomics supplies including DNA Genotek Oragene kits, 384 well plates, Taqman assays (real time/allelic discrimination)
Biological Sample Banking (DNA, whole blood, blood spots, cell lines)
Training: Provided for the 7900HT real time instrument and for project set up
Scheduling: Equipment reservations on-line through CORES. Drop-ins welcome for extraction samples or project consultation.
The CHGR DNA Resources Core provides services in human DNA extraction, sample banking, genotyping, 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, or various Illumina platforms. Links to press coverage: http://www.wsmv.com/video/22149114/ http://www.fox17.com/newsroom/fox_focus/vid_97.shtml
Contact Information Website – chgr.mc.vanderbilt.edu//page/dna-resources-core Email – [email protected] Phone - 615-936-2744
Acknowledgment Text “The Vanderbilt University Center for Human Genetics DNA Resources Core provided technical assistance for this work.” Please remember if VICTR funded your Core work to include "Supported in part by Vanderbilt CTSA grant 1 UL1 RR024975 from the National Center for Research Resources, National Institutes of Health"
Location 518 Light Hall
Vanderbilt University DNA Sequencing Facility Director: Alfred L. George Manager: Robert Woodhall
SERVICES
Sanger DNA sequencing Microsatellite Analysis Next-Generation DNA Sequencing Cell Identification Bulk PCR & Purification Robotic Liquid Handling
DNA SEQUENCING IS THE MAIN SERVICE OFFERED BY THE DNA SEQUENCING
FACILITY. THE FACILITY PERFORMS BOTH SANGER AND NEXT-GENERATION SEQUENCING
USING STATE-OF-THE-ART INSTRUMENTATION. FOR SANGER SEQUENCING, THE FACILITY
PRODUCES READ LENGTHS OF 1000 OR MORE BASES FOR HIGH QUALITY DNA
TEMPLATES. THE FACILITY USES A 454 JR. FOR DEEP SEQUENCING OF MICROBIAL
SAMPLES AND TARGETED AMPLICON RESEQUENCING. THE VANDERBILT DNA
SEQUENCING FACILITY CAN PERFORM LOW TO HIGH THROUGHPUT ANALYSIS OF
MICROSATELLITE MARKERS IN GENOMIC DNA. ANALYSIS IS PERFORMED USING THE
APPLIED BIOSYSTEMS 3730 PLATFORM FOR RAPID TURN AROUND TIME AND HIGHLY
ACCURATE ALLELE SCORING. MICROSATELLITE MARKERS HAVE MANY APPLICATIONS IN
GENETICS SUCH AS: MARKER-ASSISTED BACKCROSSING OF GENETICALLY-MODIFIED MICE
TO ESTABLISH CONGENIC STRAINS ("SPEED CONGENICS"), DISEASE GENOTYPING, AND
CELL IDENTIFICATION. THE FACILITY ALSO ALLOWS RESEARCHERS TO USE THEIR LIQUID
HANDLING ROBOTICS FOR LARGE, CUSTOM PIPETTING NEEDS. RESEARCHERS HAVE USED
THE ROBOTICS TO CREATE MULTIPLE PLATE REPLICATES AND TO CREATE 384-WELL
PLATES FROM 96-WELL SAMPLE PLATES.
CONTACT INFORMATION WEBSITE: HTTP://SEQ.MC.VANDERBILT.EDU/DNA/HTML/INDEX.HTML EMAIL: [email protected] PHONE: (615) 936 -2086
ACKNOWLEDGMENT TEXT THE AUTHORS THANK THE VANDERBILT DNA SEQUENCING FACILITY OF THE VANDERBILT
INSTITUTE FOR INTEGRATIVE GENOMICS.
LOCATION 531 LIGHT HALL
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 immuno-fluorescent 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 25 mm x 75 mm microscope slides.
Contact Information Email: [email protected] Phone: 322-0778 / 322-8453
Location Room 10420, MRB IV
The FGSR, 2010
Functional Genomics Shared Resource Director: Bill Tansey
Manager: Vicky Amann
What we can do for you:
Differential Gene Expression on a variety of Commercial Platforms
Genotyping with Affymetrix
RNAi Clones
Gene Expression Validation using Taqman Probes
Library preparation for Sequencing through the GTC
RNA Amplification using Nugen SPIA Kits
Experimental Design Consultation
Laboratory Personnel Informatics Personnel Vicky Amann, MS (Lab Manager) Zhongming Zhao, PhD (Head) Travis Clark, PhD (Head of Technology) Dedeepya Vaka, MS John Mote, MS Latha Raju, MS Chelsea Baker Blake Shester Jamaya Simmons
Contact Information Website – www.thefgsr.org Email – [email protected] Phone - 936-3003 (Lab) 936-3001 (Analysis Suite)
Acknowledgment Text All microarray experiments were performed in the Vanderbilt Functional Genomics Shared Resource. The Vanderbilt Functional Genomics Shared Resource is supported by the Vanderbilt Ingram Cancer Center (P30 CA68485), the Vanderbilt Digestive Disease Center (P30 DK58404) and the Vanderbilt Vision Center (P30 EY08126).
Location MRB III Lab: 9274 Analysis Suite: 9282
Flow Cytometry Core Director: James Crowe, Jr Manager: Kevin P. Weller
What we can do for you:
Cell Sorting – FACS Aria I & III with 405nm, 488nm, 561nm, and 635nm lasers (up to 10 colors simultaneously)
Analytical Cytometry – 2 LSRII’s with 355nm, 405nm, 488nm, 531nm and 635nm lasers (up to 17 colors simultaneously)
Flow CytometryTraining - Beginning to Advanced Magnetic Sorting - Automacs Guava EasyCyte-Cell Counting/Viability/Miscellaneous Elispot – Immunospot
Online Scheduling - Core Ordering & Reporting Enterprise System https://cfuis.mc.vanderbilt.edu/login.cfm
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 S - 0108
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Genome Technology Core
NEXT-GENERATION SEQUENCING
1. Microbial whole genome re-sequencing (DNA-seq) 2. Whole transcriptome analysis (RNA-seq) 3. Chromatin immunoprecipitation sequencing (ChIP-seq) 4. Targeted gene re-sequencing Custom target capture Human whole exome
GTC offers full service next-gen sequencing, including sample prep, sequencing, and data analysis. Services are tailored to fit each project’s needs and objectives.
GTC offers next-gen sequencing using the Illumina Genome Analyzer IIx (Solexa). 1-4 gigabases of DNA sequence per run are generated, depending on number of cycles (36-100) & single- or paired-end selections. Three existing core facilities jointly operate GTC (administered by the Office of Personalized Medicine).
Functional Genomics Shared Resource (library prep & cluster generation) [email protected]
Vanderbilt DNA Sequencing Facility (sequencing) [email protected]
Computational Genomics Core in CHGR (bioinformatics) [email protected]
Contact Information Website – gtc.vanderbilt.edu Email – [email protected] Phone – 2-4321
Acknowledgment Text The Genome Technology Core at Vanderbilt University Medical Center provided technical assistance for this work.
Location FGSR: 9274 MRB III Sequencing Facility: 531A RRB Comp Gen Core: 519LH
Illumina Genome Analysis System
High Throughput Screening Core Facility Director: David Weaver, PhD Core Manager: Lisa Wright
What we can do for you:
Assay Design and Validation
High Throughput Screening
Data Analysis
Training for Walkup Use of Plate Readers
Compound Distribution
Training: http://www.vanderbilt.edu/hts/Templates/ContactUs.htm - complete the Internal Account Form
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 www.vanderbilt.edu/hts [email protected] 936-7098
The High Throughput Screening Core Facility is part of the Vanderbilt Institute of Chemical Biology.
Location 824 Robinson Research Building
Human Tissue Acquisition and Pathology Scientific Director: Mary M. Zutter, M.D.
Managing Director: Justin M. Cates, M.D., Ph.D.
What we can do for you: Human tissue sample procurement for basic, translational, and clinical research
Pathology consultation and expertise
Full Service Histology
o Paraffin embedding and sectioning
o Frozen sectioning
o H&E and special stains
Tissue microarray construction and sectioning
Laser capture microdissection
The Human Tissue Acquisition and Pathology Shared resource (HTAP) focuses on providing human tissue samples and histology services to support translational and preclinical aspects of cancer research.
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 frozen, or in a variety of fixatives as requested by the investigator. Normal, neoplastic, and other diseased tissues are available for study.
Our full service research histology laboratory offers paraffin embedding, sectioning, automated Hematoxylin and Eosin staining, frozen sectioning and a large selection of special stains. The laboratory also offers specialized processing and sectioning services including cell block preparations, RNase free sectioning, special processing for lacZ stained samples, and tissue microarray sectioning.
The facility also offers access to a laser capture microdissection system and tissue microarray equipment.
Contact Information Website -http://www.vicc.org/research/shared/human/index.php Email – [email protected]
The Human Tissue Acquisition and Pathology Shared Resource is supported by the National Cancer Institute. Please acknowledge use of this core in any publications resulting from services performed by this facility, grant number P30 CA068485.
Location The Vanderbilt Clinic Room 4902
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 Michael Rock, Ph.D. e-mail: [email protected] Phone: 322-4494
Location Medical Center North Lab: T3316 Sample Drop-Off (cytokine analysis): S-0111 MCN
Islet Procurement and Analysis Core Director: Marcela Brissova, PhD
Research Assistant: Anastasia Golovin
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 Golovin 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 (P60 DK020593).
Location Medical Research Building IV (Langford) Room 8445C
Innovative Translational Research Shared Resource (ITR)
Director: Kimberly Brown Dahlman, PhD Laboratory Manager: Donna Hicks, 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, tissue culture, etc.)* *Subject to Advisory Board Review. Please contact Kimberly Dahlman for details.
Mission: Advance the translation of basic and clinical research into improved clinical therapies by facilitating clinical 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] Laboratory 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, Jordan Berlin, and Madan Jagasia for support.
Location 722 Preston Research Building
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 http://thecore.vanderbilt.edu [email protected] (615) 322-7238
Administered by the
Location Light Hall 834
Mouse Metabolic Phenotyping Center Fran Tripp, Program Coordinator David Wasserman, Ph.D., Director
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)
Training:
Contact Fran Tripp ([email protected]) for training information or see the Vanderbilt MMPC website (http://www.mc.vanderbilt.edu/root/vumc.php?site=mmpc)
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 www.mmpc.org [email protected] 615-343-1065
Acknowledgment Text The Mouse Metabolic Phenotyping Center is supported by NIH Grant DK59637
Location MMPC Administrative Office 843 Light Hall
Vanderbilt Sleep Research Core Director: Dr. Beth Malow
Manager: Peter Howard RPSGT
What we can do for you:
Polysomnography
Pediatric Sleep/EEG
Actigraphy
Portable Studies
Training is available on a case by case basis
Scheduling: www.mc.vanderbilt.edu/gcrc/r_sleep
The Vanderbilt Sleep Research Core Laboratory was developed to facilitate interdisciplinary research in sleep medicine. The Sleep Core offers consultation with Dr. Beth Malow and Peter Howard, RPSGT, regarding protocol development and implementation. The Sleep Core has two hard-wired state-of-the-art digital video-EEG-polysomnography systems and a third wireless system for portable studies. Two sleep technologists (Mr. Howard and Ms. Vigil) with experience in working with both adults and children carry out overnight polysomnography as well as daytime multiple sleep latency tests. Actigraphy, which assesses the sleep-wake cycle through the use of activity meters, is also available.
Contact Information http://www.mc.vanderbilt.edu/crc/sleep [email protected] Phone Pager – 615-835-1607
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 RR024975 from NCRR/NIH"
Location Building-Medical Center North Room- AA3223
Transgenic Mouse/Embryonic Stem Cell Shared Resource Directors: Mark A. Magnuson, Patricia A. Labosky, Douglas P. Mortlock
Manager: Jennifer Skelton
What we can do for you:
Pronuclear DNA Microinjections
ES Cell Injection into Blastocysts
Gene Targeting RMCE Assisted Reproduction
Techniques Rederivations
Embryo Cryopreservation Sperm Cryopreservation Cryostorage Karyotyping
BAC Recombineering
Scheduling: Visit website http://www.vanderbiltresearch.org/community/profile/id/8) to download appropriate service forms to initiate services.
Genetically-altered mice were first generated at Vanderbilt by pronuclear microinjection of DNA in 1989 and from mouse embryonic stem cells (mESCs) in 1993. Initially this Resource offered just two services: pronuclear microinjection of DNA and the microinjection of mESCs into mouse blastocysts. However, it was soon expanded and began offering gene targeting as a service in July 1995. All of these services, and several others, have been provided on a continuous basis since then. By having a single centralized facility, VUMC is able to provide quality control, the ability to develop new techniques and applications, the increased potential for collegial interactions, and access to individuals with knowledge of dealing with transgenic mice. Investigators benefit from the cost-effective services of the Transgenic Mouse/ES Cell Shared Resource focusing on the generation, maintenance and long-term storage of germline-altered mice.
Contact Information: Website: www.vanderbiltresearch.org/community/profile/id/8 Email: [email protected] Phone: 615-936-3454
Acknowledgment Text Use of the Transgenic Mouse/ES Cell Shared Resource should be acknowledged in all publications. The Transgenic Mouse/ES Cell Shared Resource is supported by the Vanderbilt Ingram Cancer Center Support Grant (CA68485), the Vanderbilt Diabetes Research and Training Center (DK20593), and/or the Vanderbilt Kennedy Center for Research on Human Development (HD15052) should be cited unless prohibited by the editorial policy of the journal.
Location: 9410 MRB IV, 2213 Garland Avenue, Nashville, TN 37232 Nashville, TN 37232
Vanderbilt Antibody and Protein Resource 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
Mammalian Recombinant Protein Production and Purification
Antibody Repository for many common and affinity tag antibodies
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 Monoclonal Antibody Core 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-related 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 of antibodies. In addition, a wide variety of specialized services related to antibody assays and usage are offered at cost with rapid turnaround. We have also recently expanded to offer large-scale recombinant protein production and purification in both bacterial and mammalian cells.
Chemical Synthesis Core Padma Portonovo (Manager) & Gary Sulikowski (Director)
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 protected] 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 37027.
Location 12410-D MRB-IV (LG) Vanderbilt University 2213 Garland Avenue
Vanderbilt Monoclonal Antibody Core 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
Mammalian Recombinant Protein Production and Purification
Antibody Repository for many common and affinity tag antibodies
Scheduling and Project Initiation: Please submit a project request form at www.vanderbilt.edu/vmac
Contact Information Website - www.vanderbilt.edu/vmac Email - [email protected] Phone - 615-936-3092 / 615-322-5623
Acknowledgment Text Antibodies/Proteins were produced/purified by the Vanderbilt Monoclonal Antibody Core. The Vanderbilt Monoclonal Antibody Core 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 VMAC mission is to make state-of-the-art antibody-related technologies cost effective and readily available to Vanderbilt Investigators. The VMAC provides reagents, equipment, protocols, and expert assistance in all aspects of production, purification, detection, and characterization of antibodies. In addition, a wide variety of specialized services related to antibody assays and usage are offered at cost with rapid turnaround. We have also recently expanded to offer large-scale recombinant protein production and purification in both bacterial and mammalian cells.
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)
Bioluminesence/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 http://vuiis.vanderbilt.edu/resources/CSAI.php Email: [email protected] Phone: 322-8352
Location Building: Medical Center North Room(s): AA-2105
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 http://www.vuiis.vanderbilt.edu/resources/human.php Email: [email protected] Phone: 322-6211
Location Building: Medical Center North Room(s): AA-0117
VUIIS Radiopharmaceutical Research Center Research Program Director: H. Charles Manning, Ph.D.
Technical Director: Michael L. Nickels, Ph.D.
What we can do for you: Provision 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, or [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: [11C]acetate (acetate metabolism, tumor imaging), [18F]fallypride (dopamine D2/D3), [
18F]FECNT (dopamine transporter), [18F]FLT (cell proliferation, nucleoside metabolism), [18F]setoperone (serotonin 5-HT2a receptor). Radiotracers for animal / in vitro studies: [18F]FP-DTBZ (vesicular monoamine transporter), , [18F]FMISO (hypoxia, tumor imaging), [18F]FPEB (mGluR5, metabotropic glutamate receptor), [64Cu]copper-ATSM (cell hypoxia, tumor imaging).
Radiotracers in Development [18F]Fluoroethylcholine, [99mTc]Tc-dextran
Radiotracer Drug Discovery Radiolabeled ligands for the peripheral benzodiazepine receptor (PBR), radioligands for amyloid protein, agonist radioligands for the dopamine D2 receptor.
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 CTI/Siemens RDS-112/00, a negative-ion cyclotron with targets and ancillary equipment optimized for generating 18F, 11C, 13N, and related radionuclides. A new cyclotron will be commissioned in late 2010. Adjacent hot laboratories utilize 2 Von Gahlen hot cells with CRL manipulators and two "dual mini-cells" housing two GE Tracerlabs FX-FN fluorination modules and an FX-C 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 and HEPA filters, is located in a separate laboratory for 123I and 125I manipulations. A Galaxie-networked system of HPLC equipment includes 3 Varian HPLC setups with UV (conventional and photodiode array) and radiometric detectors, including a Bioscan coincidence-mode metabolite detector, 2 Waters HPLC setups, and a Varian gas chromatograph. The PET Chemistry Research Lab is connected to the cyclotron through lead-shielded lines allowing direct delivery of [18F] fluoride or [11C]carbon dioxide to shielded "hot cells" for production of radiotracers. A second laboratory is located in F1200 in MCN and is dedicated to the labeling of gamma ray emitters for SPECT imaging
Contact Information http://vuiis.vanderbilt.edu/resources/chemistry.php Email: [email protected] Phone: 322-3793
Location Building: Robinson Research Room(s): 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. Training: Provided on site for registered users.
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;
Contact Information Dr. Knapik: Light Hall 1165B [email protected] Phone: 2-7569
Location ZCORE: Light Hall 109