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Core Facilities

User Handbook

2016-2017

Last updated March 15, 2016

Cores Handbook Last updated: January 2016 2

DISCLAIMER: This handbook contains general information, is not intended to be comprehensive, and the description, contact information, policies and guidance in the handbook is subject to change at any time, and with little or no warning. CORRECTIONS: Please direct any corrections or updates to Dr. Karin Scarpinato.

HANDBOOK AT-‐A-‐GLANCE

This handbook contains information for all core facility users at the University of Miami. Core facilities and shared resources are available to all

lab managers, graduate students, postdoctoral fellows and principal investigators.

You’ll find information:

▪ Contact information ▪ Core description

▪ Core campus and location ▪ Instrumentation listing ▪ Research resources

TABLE OF CONTENTS I. Introduction ........................................................................................................................ 5

II. ABOUT CORES ..................................................................................................................... 6 Division of Veterinary Resources (DVR) ............................................................................................................... 9 Drosophilia Core Facility .................................................................................................................................... 10 Humanized Mouse Core .................................................................................................................................... 11 Transgenic Animal Core ..................................................................................................................................... 12 Pathology Research Resources Histology Laboratory ........................................................................................ 13 Pathology Research Resources / Veterinary Clinical Pathology ........................................................................ 14 Zebrafish Core Facility ....................................................................................................................................... 15 BioNIUM ............................................................................................................................................................ 17 CFAR Laboratory Sciences Core ......................................................................................................................... 18 Chemistry Resources ......................................................................................................................................... 19 Clinical Chemistry, Biomarkers and Immunoassay Laboratory .......................................................................... 20 Flow Core Center ............................................................................................................................................... 21 Flow Cytometry Core ......................................................................................................................................... 22 High Content Screening Core ............................................................................................................................. 23 Live Tumor Culture Core (LTCC) ......................................................................................................................... 24 Preclinical Cell Processing and Translational Models Core Lab ......................................................................... 25 Tumor Bank Core Facility ................................................................................................................................... 26 Tissue Culture Core ............................................................................................................................................ 27 Transmission Electron Microscopy (TEM) .......................................................................................................... 28 RSMAS Tritium Laboratory ................................................................................................................................ 29 Viral Vector Core ................................................................................................................................................ 30

Biostatistics Cores .......................................................................................................................... 31 Biostatistics and Bioinformatics Core (BBC) ...................................................................................................... 32 Statistical and Bioinformatics Consulting Core (HIHG) ...................................................................................... 33

Clinical Cores .................................................................................................................................. 34 Clinical Translational Research Site ................................................................................................................... 35 Disparities & Community Outreach Core .......................................................................................................... 36 Non-‐Therapeutic Research Support (NRS) Core ................................................................................................ 37

Computational Cores ...................................................................................................................... 38 Bioinformatics and Data Mining Services .......................................................................................................... 39 High Performance Computing Services ............................................................................................................. 40 Software Engineering Group ............................................................................................................................. 41

Genomics Cores .............................................................................................................................. 42 Biorepository Core Facility (HIHG) ..................................................................................................................... 43 cGMP Cell Processing Facility (DRI) .................................................................................................................... 44 Genotyping Core Facility (HIHG) ........................................................................................................................ 45 Gene Expression Core Facility (HIHG) ................................................................................................................ 46 Oncogenomics Core Facility ............................................................................................................................... 47 Sequencing Core Facility (HIHG) ........................................................................................................................ 48 Center for Advanced Microscopy (UMCAM) ..................................................................................................... 50 Analytical Imaging Core Facility ......................................................................................................................... 51 Confocal Microscopy Core/Molecular Core Lab ................................................................................................ 52 Imaging and Histology Core ............................................................................................................................... 53 Neuroimaging Facility ........................................................................................................................................ 54

Marine Operations ......................................................................................................................... 55 RSMAS Marine Operations ................................................................................................................................ 56

Cores Handbook 2016-‐2017 Last updated: March 2016 University of Miami 4

IV. Emergency Management .................................................................................................. 57

V. Research Resources at the University of Miami ................................................................. 58 Libraries ............................................................................................................................................................. 58 Office of Research .............................................................................................................................................. 59 Environmental Health and Safety, Radiation Safety, and Animal Welfare ........................................................ 59 Human Subject Research Office ........................................................................................................................ 59 Intellectual Property and Licensing ................................................................................................................... 60 Research Listservs .............................................................................................................................................. 60


I. Introduction

The University of Miami was established in 1925 and is highly recognized for its significant contributions to research. The university’s mission is to educate and nurture students, to create knowledge, and to provide service to our community and beyond. Committed to excellence and proud of our diversity of our University family, we strive to develop future leaders of our nation and the world. Counting more than 171,000 alumni in fields spanning from architecture to marine zoology, the University of Miami is proud to have produced some of the nation’s and world’s most successful researchers in academia and industry.

The University of Miami is engaged in $360 million in research and sponsored programs a year with the majority housed at the Leonard M. Miller School of Medicine. The School of Medicine is an academic medical center founded in 1952 with more than 1 million patient encounters annually. The Rosenstiel School of Marine and Atmospheric Science is one of the leading oceanographic and atmospheric research institutions in the world. The marine campus is located on Virginia Key and is part of a specially designated 65-‐acre marine research and education park that includes two NOAA laboratories. At the Coral Gables campus investigators conduct research in engineering, education, and psychology. Office of Research Administration The Office of Research facilitates the UResearch community’s scholarly activity, scientific discovery, and the responsible conduct of research by providing an integrated network of support and educational opportunities, including specialized facilities, assistance in obtaining and managing extramural funds, and administrative oversight of all regulatory aspects of research operations.

Research, Research Education and Innovative Medicine (RIM) Our mission is to facilitate life-‐changing discoveries and advance patient care through: innovative research, education of the next generation of research leaders.

1

Coral Gables Campus

CORES HANDBOOK


II. ABOUT CORES The University of Miami recognizes the importance of maintaining a variety of specialized facilities and instrumentation to support the growing research and education enterprise. Shared and core facilities are created and directed by UM faculty and supported by the university to facilitate interdisciplinary collaboration. Core facilities at the University of Miami are located across its three campuses: the Leonard M. Miller School of Medicine, Coral Gables and the Rosenstiel School of Marine and Atmospheric Science (RSMAS) and are housed across different departments and centers. What is a core facility? Core facilities are centralized shared research resources that provide access to instruments, technologies, services, as well as expert consultation and other services to scientific and clinical investigators. The typical core facility is a discrete unit within an institution and may have dedicated personnel, equipment, and space for operations. In general, core facilities recover their cost, or a portion of their cost, of providing service in the form of user fees that are charged to an investigator's funds, often to NIH or other federal grants. What is a shared resource? Shared resources include informal resources, shared/common equipment, formalized service centers, and core facilities. Guidelines for authorship on manuscripts There are many important reasons to acknowledge contributions from core facilities in publications. The The Association of Biomolecular Resources (ABRF) guide provides useful practices for core laboratories. You can access the guide at: http://pcf-‐ptp.epfl.ch/files/content/sites/pcf-‐ptp/files/Documents/ABRF_Guidelines.PDF

2 CORES HANDBOOK


III. ABOUT THE USER HANDBOOK

The Cores Handbook is designed to provide at-‐a glance information on core facilities, including how to contact the core facility scientists, where the core is located, a brief description of cores services, and a listing of instrumentation at the core. Contact the core for more information on services and prices. To view a complete list of cores and shared resources, visit the Core Facilities and Shared Resources website: http://uresearch.miami.edu/research-‐resources/core-‐facilities. If your core facility is not listed in the handbook or if you need to submit corrections, please email Dr. Karin Scarpinato.

At-‐a-‐glance legend

Center

The name of the center of department where the core is located: College of Arts and Sciences, Miami Project to Cure Paralysis, Sylvester Comprehensive Cancer Center, Diabetes Research Institute, Department of Pathology, Hussman Institute for Human Genomics, and other departments.

Type

Cores are grouped by type: animal, biochemical, biostatistics, clinical, computational, genomics, imaging, and marine operations.

Contact

Point of contact for the core, which can vary, from the core director or core manager, or a generic contact.

Campus

Coral Gables; Leonard M. Miller School of Medicine; or Rosenstiel School of Marine and Atmospheric Science (RSMAS).

Location

Name of building, and room number. Inquire with the core, if location is not listed.

Training Required

States if training is required to use the core or equipment.

Access

Open or closed, describes whether a core is open to any user, restricted to a specific set of users, or if a user needs to inquire on access.


3

Animal Cores

Division of Veterinary Resources

Drosophila Core Facility

Histology Laboratory

Humanized Mouse Core

Transgenic Animal Core

Veterinary Clinical Pathology Laboratory

Zebrafish Core Facility


DIVISION OF VETERINARY RESOURCES (DVR)

What we can do for you

§ Animal care and welfare of animals used in biomedical research and teaching (cleaning, feeding, and housing.

§ Research support services including surgical anesthesia, and procedural support, rodent colony management, minor procedures, protocol consultation, experimental design assistance, budgeting, necropsy and tissue collection, phlebotomy, other diagnostics.

§ Regulatory compliance assistance.

Instrumentation

§ Various animal housing types, by species § Surgical and anesthesia equipment

Core Director Julia Zayas, Ph.D. Type

Contact Animal Core [email protected] / (305) 243-‐2310

Campus/Department Leonard M. Miller School of Medicine Location Biomedical Research Building, 200 Main Office

Training Required Animal handling and care, veterinary licensure (vets) Access Open

Contact the

Core


DROSOPHILIA CORE FACILITY


§ Stocks can be maintained for individual labs at the core facility § We provide fly food for maintaining Drosophila stocks § Services prices: $39.50 per box (100 vials); $1.75 per bottle; Drosophila strain maintenance:

$28.00 per 10 stocks per month Instrumentation

§ High-‐throughput screening (HTS) Drosophila media maker

Core Director

Grace R. Zhai, Ph.D.

Core Manager Zoraida Diaz-‐Perez Contact [email protected] / (305) 243-‐6058

Campus/Department Leonard M. Miller School of Medicine, Department of Molecular and Cellular Pharmacology

Location RMSB 6062A Training Required Inquire

Access Closed

Contact the

Core


HUMANIZED MOUSE CORE

What we can do for you The overall goal of this core facility is to provide the infrastructure, reagents, animals, technical expertise and research support services that will facilitate the se of humanized immunodeficient mice in studies examining pathogenesis and treatment of cancer and infectious disease. Humanized Mouse Core aims are to provide:

§ Study-‐ready cohorts of immunodeficient mice reconstituted with human lymphohematopoietic cells.

§ Technical expertise, training, and consultation on the use of humanized mouse models, including, training on care and handling of humanized mice

§ Consultation on study design and analytical techniques (FACS, IHC, Q-‐PCR), § Technical support for IACUC/IBC protocols, grant proposals, preliminary data

Instrumentation

§ Immunodeficient NOD/SCID/interleukin-‐R gamma chain knockout (NSG) mice are reconstituted with human lymphohematopoietic cells and tissues

§ hu-‐PBMC NSG: reconstituted with human peripheral blood mononuclear cells (PBMC) § hu-‐CD34+ NSG: reconstituted with human CD34+ hematopoietic stem/progenitor cells (HSPC) § hu-‐BLT NSG: reconstituted with human CD34+ HSPC and fetal liver / thymus tissues

Core Director

Noriyuki Kasahara, MD, Ph.D.

Core Manager Katrin Hacke, Ph.D. Contact [email protected]

[email protected] Campus/Department Leonard M. Miller School of Medicine

Location Papanicolaou Building, Room 410 Training Required Animal care & use / blood-‐borne pathogen training

Access Inquire Contact the

Core


TRANSGENIC ANIMAL CORE

What we can do for you The Transgenic Animal Core facility aims to provide a comprehensive set of methodologies and support in every aspect of generation of transgenic and targeted mutation mice. Services:

§ Molecular biology § ES Cell Culture § Mouse Embryo Manipulation § Mouse Preservation and Storage § Transgenic Animal Services in Development

Instrumentation

§ Zeiss Telaval 31 Inverted Microscope § Olympus IMT-‐2 Inverted Microscope § Zeiss Axiovert 100TV inverted microscope § Dissecting Stereoscopic Microscopes § Baker Tissue Culture Hood § C02 Incubators § BTX ECM 630 Electroporator § Hamilton Thorne XYClone Laser Ablator

Core Director

Yingcai Wang, Ph.D.

Core Manager Maritza Inza Contact [email protected]

(305) 243-‐5890 Campus/Department Leonard M. Miller School of Medicine

Location Gautier, Room 638 Training Required Inquire

Access Inquire

Contact the

Core


PATHOLOGY RESEARCH RESOURCES HISTOLOGY LABORATORY


§ Routine histology services including processing/embedding, sectioning, H&E staining, and coverslipping

§ Frozen sectioning (by histotechnologist or by investigator) § Immunohistochemistry § Special processing and embedding as needed for final presentation of tissue type § Sectioning to produce paraffin curls for RNA or DNA analysis § Special staining § Animal necroscopy guidelines and assistance in experimental design § Sectioning of archived blocks for retrospectice studies on human tissues

Instrumentation

§ Crysostat § Embedding machine § Processor

§ Microtomes § Automatic Slide Stainer § Coverslipper

Core Director

Norman Altman, VMD

Core Manager Carolyn Cray, Ph.D. Contact [email protected]


Location RMSB 7101A Training Required No open use of equipment except for cryostat;

training provided Access Open

Contact the

Core


PATHOLOGY RESEARCH RESOURCES / VETERINARY CLINICAL PATHOLOGY


§ Routine clinical pathology testing include complete blood count (CBC) and biochemistry panels § Specialized testing on request including hormone analyses, protein electrophoresis, and more § Specialized chemistry determinations § Assistance in experimental design and test interpretation § Animal necropsy services and review of histology by board certified veterinary pathologist

Instrumentation

§ Hematology analyzer § Chemistry analyzer (Dry) § Gamma counter § ELISA reader § Semi-‐automated protein electrophoresis § Microscopes Chemistry analyzer (Wet)

Core Director

Norman Altman, VMD

Core Manager Carolyn Cray, Ph.D. Contact [email protected]


Location RMSB 7101A Training Required All services completed by lab staff

Access Open

Contact the

Core


ZEBRAFISH CORE FACILITY


§ Consult and train individuals in using zebrafish as an animal model § Import transgenic lines useful for your experiments § House adult fish § Provide daily embryos for experiments § Provide injection set-‐ups adjacent to the animal room for experiments § Raise transgenic lines or CRISPR mutant lines that you generate § http://www.as.miami.edu/faculty-‐and-‐staff/zebrafish/

Instrumentation

§ 444 sq. ft. room housing 20 racks of recirculating aquaria (Aquatic Habitat). § A mechanical equipment room houses water reservoirs, pumps, filters, and UV sterilizing

equipment, as well as automatic monitoring and dosing equipment to maintain stable water chemistry.

§ A prep room houses a dishwasher to clean tanks and a refrigerator to store food. The facility also counts on an enclosure for hatching live brine shrimp to feed the zebrafish.

§ A quarantine room with an independent set of aquaria for import of lines § Three injection set-‐ups with MPPI-‐3 foot-‐pedal-‐triggered pressure injectors, micromanipulators,

dissecting scopes and light supplies

Core Director

Julia Dallman, Ph.D. and Zhongmin Lu, Ph.D.

Core Manager Ricardo Cepeda Contact [email protected] or [email protected]

(305) 284-‐3954 or 6881 Campus/Department Coral Gables Campus

Location Cox Science Center, Room 40 Training Required Prior to conducting experiments with zebrafish, new users

require one or two training sessions with Dr. Dallman or Dr. Lu Access Closed

Contact the

Core


Biochemical Cores

BioNIUM

CFAR Laboratory Sciences Core

Chemistry Resources

Flow Core Center (DRI)

Flow Cytometry Core

High Content Screening Core

Live Tumor Culture Core (LTCC)

Tumor Bank Core Facility (TBCF)

Tissue Culture Core

Transmission Electron Microscopy (TEM)

RSMAS Tritium Laboratory

Viral Vector Core


BIONIUM

What we can do for you The BioNIUM Nanofabrication Facility (Biomedical Nanotechnology Institute) is training the next generation of scientific leaders to fabricate microscale biomedical devices, perform breakthrough research and create far-‐reaching enabling technologies. Instrumentation The Facility houses more than 20 state-‐of-‐the art equipment, some salient ones include:

§ Electron Beam Lithography § Scanning Electron Microscope § Electron Beam Evaporator § Sputter § Plasma Enhanced Chemical Vapor Deposition § Inductively Coupled Plasma/Ion Reactive Etcher § Mask Aligner § Mask Maker § Surface Profiler § Wire Bonder

Core Director

Ram H. Datar, Ph.D.

Core Manager Jaesun Lee, Ph.D. Contact [email protected]


Location Life Science & Technology Park, Suite 460 Training Required All equipment requires training to operate. Once authorized, users can

operate equipment themselves. Access Open Contact the

Core


CFAR LABORATORY SCIENCES CORE What we can do for you

§ Cell subsets and maturation markers based on surface phenotype in blood and tissues using 15 color flow cytometry (Cell types: T, B, NK, Monocytes, other)

§ Cell functions: proliferation, cytokine expression and secretion, using flow cytometry and Elispot assays for B and T cells

§ Single and Multiplex analysis of protein biomarkers (cytokines, gut microbial translocation markers, etc.) using Luminex Magpix system or ELISA

§ User-‐friendly six color sorting using chip based Sony SH800 sorter § Transcriptomic analysis for RNA and single cell gene expression using Fluidigm BioMark and C1

autopreDetection of HIV infected cells by p24 ELISA in culture supernatants § Cell associated HIV DNA and RNA using digital droplet PCR and Viral Sequencing for phylogenetic

analysis § Purified human blood products (PBMC, T or B lymphocyte subsets, monocytes and dendritic

cells, plasma and serum) § Specimen bank for cells, plasma and serum

Instrumentation

§ Fluidigm Biomark and C1 single cell autoprep for multiplex real time PCR § Sony SH800 Sorter § BioRad QX100 Digital Droplet PCR with FAM (EvaGreen) and HEC (VIC) detection channels § Sequencher software § Luminex Magpix multiplex system § StepOne real time PCR § Becton Dickinson FACSCalibur

Core Co-‐Directors

Savita Pahwa MD; Co-‐Director, Siôn Williams, Ph.D.

Core Manager Margie Roach, Ph.D. Contact [email protected] / (305) 243-‐4822

Campus/Department Leonard M. Miller School of Medicine Location Batchelor Children’s Research Institute, Room 708

Training Required Training required for to use Sony SH800 Cell Sorter

Access Open

Contact the

Core


CHEMISTRY RESOURCES


§ Routine NMR spectroscopy on purified, prepared samples submitted in 5mm tubes § Routine ESI Mass spectroscopy on purified, prepared samples § Limited processing for EPR, FTIR, and other instruments § Fee schedule visible at http://www.as.miami.edu/chemistry/research/fees/

Instrumentation

§ Bruker 500, 400, 300 NMRs § Bruker Micro-‐TOF-‐Q mass spectrometer § Bruker EMX EPR § Various Perkin Elmer, Agilent instruments

Core Director

David Hudson, Ph.D.

Contact [email protected] / (305) 284-‐3862 Campus/Department Coral Gables Campus

Location Cox 348 Training Required Please contact director before submitting samples

Access Closed

Contact the

Core


CLINICAL CHEMISTRY, BIOMARKERS AND IMMUNOASSAY LABORATORY What we can do for you The laboratory performs assays for the determination of metabolic control, hormone levels and disease biomarkers in human blood, urine and saliva samples. The laboratory is licensed by the state Florida and is CLIA certified. All methods are validated and strict adherence to quality control is maintained to provide reliable and reproducible data.

§ Diabetes Monitoring: Glucose, Hemoglobin A1c, Insulin, C-‐peptide, Proinsulin, Glucagon § Lipoprotein Monitoring: Serum Lipid Profiles, apolipoproteins A-‐I, B, C-‐II, C-‐III, Lp(a) § Routine Chemistry Monitoring: Electrolytes, liver and renal function § Cardiovascular Risk Biomarkers: soluble-‐ICAM, VCAM, E-‐selectin, P-‐selectin, NT-‐pro-‐BNP,

Troponin § Inflammatory Biomarkers: C-‐Reactive Protein, IL-‐6, MCP-‐1, TNF-‐α § Adipokines: Adiponectin, leptin § Endocrine Testing: Thyroid, PTH, steroid hormones, cortisol, oxytocin. § Additional Services: Processing of samples prior to analysis. Establishment and validation of

new tests as required for specific projects.

Instrumentation

§ Roche Cobas 6000 Chemistry and Immunoassay Analyzer § ELISAa plate washers, Visible, UV, fluorescent and chemiluminescent plate readers. § Gamma counter for RIA

Core Director

Armando J. Mendez, Ph.D.

Core Manager Esperanza Perez Contact [email protected] / (305) 243-‐5314

Campus/Department Leonard M. Miller School of Medicine, Diabetes Research Institute Location Diabetes Research Institute, 3033

Training Required Lab personnel perform all measurements Access Open

Contact the

Core


FLOW CORE CENTER What we can do for you Consulting and experimental design:

§ Instrument and Software training § Sample acquisition on BD LSRII and Beckman Coulter CytoFlex § High speed cell sorting on Beckman Coulter MoFlo Astrios EQ § Data analysis using FACSDiva, FlowJo, ModFit LT, Kaluza, CytExpert, and Summit § Data interpretation and figure generation for grants and publications § Data storage on dedicated server

Instrumentation

§ BD LSRII equipped with 405, 488, 532, and § 640nm Laser lines (20 parameters and 18 colors) § CytoFlex equipped with 405, 488, 561, and 640nm Laser lines (15 parameters and 13 colors) and 96 well

plate loader. § MoFlo Astrios EQ* high speed cell sorter equipped with 355, 405, 488, 561, and 640nm Laser lines (27

parameters and 22 colors. § Provides 6 way sorting at a speed of up to 70k event per second at 60psi using a 70um nozzle § (Note: Sort speed decreases significantly with larger nozzle size). Available Nozzle sizes are:

70, 100, 200, and 400um. Index sorting and single cells deposit into up to 1536 well plates. Dual Forward Scatter PMT allows simultaneous display and sorting of small and large particles. The Astrios will be housed in Class II biosafety cabinet for BSL-‐2 and BSL2+ applications.

Core Director

Oliver Umland, Ph.D.

Contact [email protected] / (305) 243-‐9768 / Lab: (305) 243-‐1097 Campus/Department Leonard M. Miller School of Medicine, Diabetes Research Institute

Location DRI, 2nd Floor Lab, Room 2030, Office: 2014 Training Required BD LSRII and Beckman Coulter CytoFlex may be used 24/7 by trained users

Access Inquire

Contact the

Core


FLOW CYTOMETRY CORE What we can do for you The Flow Cytomerty Core Facility provides researchers with sophisticated methods for the analysis and preparative sorting of a wide variety of cell, under many experimental conditions.

The facility is able to measure:

§ Cellular parameters such as apoptosis § Gene expression § Drug metabolism § Immune responses and pathways of cellular activation

Instrumentation

§ Becton Dickinson (BD) FACS Canto-‐II, 8 color analyzer § BD LSR-‐II, 10 color analyzer § BD LSR-‐Fortessa-‐HTS, 19 color, high-‐throughout analyzer § Partec CyFlow Space, 6 colour analyzer and cell counter § BD FACS Aria I, 8 color cell sorter § BD FACS Aria IIu, 17 color cell sorter § BCI MoFlo XDP, 7 color, high-‐speed cell sorter, in BSL-‐2 cabinet § Zeiss fluorescence microscope, with camera § Invitrogen Countess, cell counter and viability analyzer

Core Director

Huw S. Kruger, Ph.D.

Contact [email protected] / (305) 243-‐5019 Campus/Department Leonard M. Miller School of Medicine, Sylvester Comprehensive Cancer Center

Location Rosenstiel Medical Science Building, Room 3061 Training Required Basic training, on a monthly basis, plus advanced training on-‐demand, in

theory, practice, and application of flow cytometry, as well as in the analysis of flow cytometric data.

Access Open

Contact the

Core


HIGH CONTENT SCREENING CORE

What we can do for you The High Content Screening (HCS) Core provides a cutting edge, multiplexed functional screening and imaging platform to perform multi-‐well cell-‐based assays.

Instrumentation

§ ThermoFisher Cellomics § ArrayScan VTI instrument § Automated cellular analysis software

Core Director

Vance Lemmon, Ph.D. and John Bixby, Ph.D.

Core Manager Yan Shi Contact [email protected] / (305) 243-‐1951

Lab: (305) 243-‐1097 Campus/Department Leonard M. Miller School of Medicine / Miami Project to Cure Paralysis

Location Lois Pope Life Center, Room 4-‐03 Training Required The instrument is operated by core staff but the staff can provide training in

data analysis and offer guidance on assay development and plate handling

Access Open

Contact the

Core


LIVE TUMOR CULTURE CORE (LTCC)

What we can do for you The goal of LTCC is to provide the research community with:

§ Primary Normal Human Cell Lines § Primary Normal Tumor Cell Lines § Custom Medium § Viably Preserved Tumor Cell Ready for Establishing Cell Lines

Cell Lines

§ Primary Human Ovarian Carcinoma § Normal Immortalized Ovary § Transformed Ovary § Tumorigenic Ovary § Normal Immortalized Breast § Transformed Breast

§ Tumorigenic Breast § Normal Immortalized Fallopian Tube § Transformed Fallopian Tube § Tumorigenic Fallopian Tube § Other Developing

Custom medium: OCMI-‐L; OCMI-‐Le; FOMI; BMI-‐P; BMI-‐I; and other developing medium

Core Director

Tan A. Ince, MD, Ph.D.

Contact [email protected] / (305) 243-‐4608 Campus/Center Leonard M. Miller School of Medicine, Sylvester Comprehensive Cancer Center

Location Biomedical Research Building (BRB), Room 911.01 Training Required Inquire

Access Open

Contact the

Core


PRECLINICAL CELL PROCESSING AND TRANSLATIONAL MODELS CORE LAB What we can do for you The Preclinical Cell Processing and Translational Models Core Lab serves as a resource for Diabetes Research Institute and University of Miami investigators and collaborators, providing support in the design and execution of experiments utilizing small animal models of diabetes and cellular transplantation. Rodent (Mice or Rat) Islet isolation Cell or Islet transplantation in rodents:

§ Renal Subcapsular Space § Subcutaneous § Intraperitoneal § Intraportal § Metabolic Assays: Glucose or Insulin Tolerance § Monitoring and care of rodents, including: § Urine and Blood Glucose Monitoring § Administration of Treatments § Necropsy and sample collection

Instrumentation

§ Surgical instruments available § Light sources § Dissecting microscopes

Core Director

Joel Szust, Ph.D.

Core Manager Yelena Gadea Contact [email protected] / (305) 284-‐2924

Campus/Department Leonard M. Miller School of Medicine Location Diabetes Research Institute, 2016

Training Required Upon request Access Open

Contact the

Core


TUMOR BANK CORE FACILITY

What we can do for you The Tumor Bank Core Facility (TBCF) is designed to facilitate translational cancer research by procuring and banking specimens and normal control tissues, with the associated clinical data, for all UM investigators and Sylvester Comprehensive Cancer Center members. TBCF banks tissue and paired clinical data for UM investigators who have IRB approval.

Services UM investigators who wish to utilize tumor tissue and data from the bank are asked to provide 1) an IRB approval or exemption letter for the project, and 2) a proposal for the use of requested tissues. Once the request is approved by the appropriate TBCF Adjudication Committee de-‐identified tissue samples and the appropriate clinical history are obtained for the investigator. Tissue collected through the bank is available to all UM investigators. Tissue collected for a specific study is made available with the permission of the PI.

Equipment

§ -‐80°C freezers (4) § -‐20°C freezer § 4°C refrigerator § LN2 storage § Galileo CK3500 TMA System § 2 headed Reichert light field microscope § Computers and software (CaTissue/Brady) for bar coding and data storage

Core Director

Tan Ince, M.D., Ph.D.

Core Manager Lynn Herbert Contact [email protected] / [email protected] / (305) 243-‐6777

Campus/Department Leonard M. Miller School of Medicine Sylvester Comprehensive Cancer Center

Location Fox Building, Room 436, 1550 NW 10th Avenue Training Required Inquire

Access Open

Contact the

Core


TISSUE CULTURE CORE What we can do for you The Biology Department Tissue Culture Core Facility is fully equipped to do both cell and tissue cultures. The facility is equipped to study developmental biology using the chicken embryo model. Injection and electroporation equipment is available for tissue manipulation of chicken embryos.

Instrumentation

§ Thermo Forma Class II Biosafety cabinet, 4 foot § NuAire Horizontal (Laminar) flow cabinet, 4 foot § Thermo Forma 37° C, CO2 incubator § Labline incubator § Refrigerator and -‐20° C freezer § Inverted microscopes § Dissecting microscopes with light sources (3) § Square wave electroporation units (2) § Micro injector and capillary glass electrode puller (available) § Avian egg incubator § Refrigerated incubator § Liquid nitrogen cryogenic storage unit § Centrifuges § 37° C water bath § Consolidated autoclave (available) § Barnstead Ultrapure water system (available) § Lonza/ Amaxa Nucleofector system (available)

Core Director

Linda White, Laboratory Manager

Contact [email protected] / (305) 284-‐2494 Campus/Department Coral Gables Campus, Biology Department

Location Cox Science Center, Room 229 Training Required Proof of attendance of the Environmental Health and Safety

Department's Laboratory Safety, and Biological Safety webinars is required. The use of recombinant DNA requires an approved IBC protocol. No virus work is allowed in the facility.

Access Closed Contact the

Core


TRANSMISSION ELECTRON MICROSCOPY (TEM) What we can do for you

§ Processing of block tissue, tissue cultures, cell pellets and exosomes for transmission electron microscopy.

§ Embedding of immunostained tissue and tissue for immunogold staining is also provided. § Training users on processing techniques, ultra-‐microtomy and electron microscope use.

Instrumentation

§ JEOL JEM-‐1400 § Philips CM-‐10

Core Director

Margaret Bates, Ph.D.

Core Staff Vania Almeida and Yelena Pressman Contact [email protected]

[email protected] / (305) 243-‐7137 Campus/Department Leonard M. Miller School of Medicine, Miami Project to Cure Paralysis

Location Lois Pope Building, Rooms 4-‐34 and 5-‐23/24 Training Required Independent users must be trained by the TEM core


Core


RSMAS TRITIUM LABORATORY What we can do for you

§ Environmental aqueous or gas phase measurements of Tritium, Sulfur Hexafluoride, CFC-‐11, CFC-‐12, CFC-‐113 and Carbon Tetrachloride.

§ Low-‐level tritium and carbon-‐14 contamination measurements.

Instrumentation

§ Custom built gas proportion counters for tritium measurement § Custom built purge and trap gas chromatographs for SF6, CFC and CCl4 measurements § Packard 2910TR Liquid Scintillation Counter

Core Director

Jim Happell, Ph.D.

Contact [email protected] / (305) 421-‐4110 Campus/Department Rosenstiel School of Marine and Atmospheric

Science (RSMAS) Location Tritium Lab Building

Training Required None Access Open

Contact the

Core


VIRAL VECTOR CORE What we can do for you

§ Lentivirus production (Full prep and half prep) § AAV particle production (FPLC-‐purified) (Full

prep and half prep) § Aliquots of Stock AAV (10uL/vial) § Aliquots of Stock Lenti (20uL/vial) § Maxiprep plasmid preparation

Core Director

Vance Lemmon, Ph.D.

Core Manager Pingping Jia Contact [email protected] / (305) 243-‐0407

Campus/Department Leonard M. Miller School of Medicine, Miami Project to Cure Paralysis Location Lois Pope LIFE Center, Room 426A

Training Required IBC approval to use lentivirus and AAV Access Inquire

Contact the

Core


Biostatistics Cores

Biostatics and Bioinformatics Core (BBC)

Statistical and Bioinformatics Consulting Core


BIOSTATISTICS AND BIOINFORMATICS CORE (BBC)

What we can do for you The main aim of this core is to incorporate aspects of high-‐throughput and high-‐performance computing with knowledge discovery approaches through application of sound statistical methods. The BBC provides cutting edge, state of the art biostatistical and computational expertise for cancer research. BBC support is available to Cancer Center members. Members of the BBC provide expertise ranging from statistical design and analysis, to computational support for high throughput data analysis. The Biostatistics Division provides statistical expertise for a broad range of oncology research including clinical trials, basic science investigations, and population studies. The Bioinformatics Division provides analytical expertise on biological data. BIOSTATISTICS SERVICES

§ Pre-‐award (Grants, LOIs, Clinical Trial Protocols) -‐ Design of clinical and population studies and laboratory experiments: Recommendations for selecting a study design; Sample size determination and justification; Statistical analysis plan for interim and final results; Early stopping guidelines for data and safety monitoring; Write-‐up of statistical considerations for grants and protocols.

§ Post-‐award -‐ Data analysis and interpretation of findings throughout the project; Write-‐up of statistical methods and results for manuscripts, abstracts, presentations, and reports to oversight committees and funding agencies; Consultation for database design and data management; Assistance with protocol amendments.

BIOINFORMATICS SERVICES

§ Gene expression analysis from commercial microarray platforms and custom-‐made cDNA arrays; Next-‐Generation Sequencing Analysis; Pathways and System biology Analysis; Prognostic Biomarker discovery using microarray and proteomics data; miRNA analysis and Nanostring; SNP functionality e.g. change of the protein structure or the structure of the promoter region.

Technologies

Biostatistics Technologies § Statistical software (commercial): SAS, SPSS, PASS, NCSS, GESS, MS Excel developed modules: BAYES-‐R,

BAYES-‐S, BERT and SET. § Database software: MS Access and REDCap § Public domain software: R, SEER*Stat, EWOC (Bayesian dose escalation / de-‐escalation), PH1ATD (analysis

of Phase I trials with accelerated titration designs), OTSD (optimal two-‐stage designs for Phase II clinical trials), STPLAN (study planning calculations).

Bioinformatics Technologies

§ GeneSpring GX from Agilent § MetaCore from GeneGo § Genomatix Promoter Inspector § TIBCO Spotfire § IBM eserver 1350 cluster, and IBM p-‐

575 cluster, are available for data analysis.

§ R tools & Bioconductor § Matlab § NCBI Toolkit § RealTime StatMiner (R) § 5040-‐core Linux Xeon/X86_64 Computational Cluster

Core Director

Xi Steven Chen, Ph.D.

Core Manager Lola Summer, MA Contact [email protected] / (305) 243-‐3957

Campus/Department Leonard M. Miller School of Medicine, Sylvester Comprehensive Cancer Center

Location CRB 1050 and Fox 303 Training Required Inquire

Access Inquire


STATISTICAL AND BIOINFORMATICS CONSULTING CORE (HIHG) What we can do for you The Statistical and Bioinformatics Consulting Core within the Center for Genetic Epidemiology and Statistical Genetics (CGESG) at the John P. Hussman Institute for Human Genomics (HIHG) provides start to finish support for genomic analysis. Our team of bioinformaticians, genetic epidemiologists, and statistical geneticists provide assistance in all aspects of project analysis including study design, quality control, statistical analysis, and interpretation of results to assistance with manuscripts and grant applications.

§ Study Design § Next Generation Sequencing Bioinformatic Analysis

• DNA sequencing (Genome, Exome, Custom) • RNA sequencing (differential expression, splicing) • Methylation sequencing (differential methylation) • ChIP sequencing (differential peak calling) • Metagenomics (16S profiling, whole metagenome analysis)

§ Statistical Analysis

• Association (GWAS, candidate gene, metaanalyses, gene environment) • Linkage • Sequencing statistics (summaries, gene-‐based association, familial analysis) • Pathway analysis (gene set enrichment, MetaCore) • Gene expression (RNAseq, microarray) • DNA methylation (methylation chip analysis

Center

Core Director

John P. Hussman Institute for Human Genomics (HIHG) Eden Martin, Ph.D.

Core Staff Anthony Griswold Contact [email protected] / (305) 243-‐5982

Campus/Department Leonard M. Miller School of Medicine Location Biomedical Research Building, Room 428

Training Required Inquire Access Closed

Contact the

Core


Clinical Cores

Clinical Translational Research Site

Disparities & Community Outreach Core

Non-‐Therapeutic Research Support (NRS) Core


CLINICAL TRANSLATIONAL RESEARCH SITE What we can do for you The CTRS offers two comfortable, easily accessible locations for investigators to conduct professional, high quality and safe research involving human subjects.

§ Facilitate both in-‐patient and out-‐patient study visits with exam rooms, phlebotomy/infusion rooms, and laboratory for specimen processing.

§ CTRS nurses and technicians provide services that include clinical research protocol implementation and data collection; routine sample collection, processing and shipment; and other research-‐related study assessments and evaluations.

Facilities and Resources

§ Clinical examination rooms equipped with an exam table, infusion chair, vital signs monitor, and sink § Phlebotomy/infusion room equipped with infusion chairs § Interview rooms equipped with internet access, table and chairs § Specimen processing room equipped with refrigerated centrifuge, refrigerator and a -‐20°C freezer § Specimen storage room equipped with a -‐80°C freezer § Pulmonary Function Laboratory § 12-‐lead ECG § Dual-‐energy X-‐ray absorptiometry (DEXA): body composition (lean and fat mass) and bone mineral density

Core Director

Matthias Salathe, M.D.

Core Manager Joanne Krasnoff, Ph.D., Operations Manager Nurse Manager Halina Kusack, RN

Contact (305) 243-‐5012 Campus/Department Leonard M. Miller School of Medicine

Location University of Miami Hospital, 7th Floor, south wing Training Required Not applicable

Access CTRS IRB ancillary committee review required Contact the

Core


DISPARITIES & COMMUNITY OUTREACH CORE What we can do for you The Disparities and Community Outreach Core provides services to support community-‐based and disparities-‐focused research at Sylvester. The core provides services that help researchers work with populations that contribute to the cultural, racial and ethnic diversity of South Florida. The South Florida area, which includes Miami-‐Dade, Broward, and Palm Beach counties, is one of the most racially/ethnically and socio-‐economically diverse metropolitan areas in the United States. Minority, low income, and immigrant population sub-‐groups in this area contribute disproportionately to cancer morbidity and mortality.

§ Participant Recruitment and Retention § Data Collection § Project Management § Database design § Training and Education § Data entry and Management § Transcription and Translation Services § Protocol Development and Regulatory Support § Pre-‐award services (community and cancer profiles, letter of support)

Instrumentation

§ Electronic devices including laptops and iPads § Software for qualitative and quantitative data entry and statistical analysis, § Database system for project development and training § Digital recording equipment for interviews and focus groups.

Core Director

Martine Poitevien

Contact (305) 243-‐4630 / [email protected] Campus/Department Leonard M. Miller School of Medicine, Sylvester Comprehensive Cancer Center

Location Clinical Research Building, Room 1004, 1120 NW 14th Street, Miami, FL 33136 Training Required Community based participatory research, Cancer and Health Disparities

Access Open

Contact the

Core


NON-‐THERAPEUTIC RESEARCH SUPPORT (NRS) CORE What we can do for you The Non-‐Therapeutic Research Support (NRS) Core provides research support services by skilled research professionals to non-‐therapeutic research projects being conducted at the Cancer Center. NRS Core Services include: Enrolling participants

§ Screening for eligible participants through electronic medical record (at JMH & Sylvester § Serving as liaison with referring physicians during clinic (all oncology specialties) § Conducting in-‐clinic recruitment (face-‐to-‐face) and phone screenings § Obtaining informed consent

Data Collection

§ Administer surveys § Conduct interviews (including SCID and other psychiatric diagnosis scales) § Facilitate focus groups § Quality control checking § Specimen transport § General Research Coordination Activities § Duties related to study administration and interventions § Intervention Delivery by a skilled Facilitator

General Research Coordination Activities

§ Duties related to study administration and interventions § Intervention Delivery by a skilled Facilitator

Core Co-‐Directors

Noella Dietz, Ph.D. and Suzanne Lechner, Ph.D.

Core Manager Madeline Krause, MS, Ed. Contact (305) 243-‐3329 / [email protected]

Campus/Department Leonard M. Miller School of Medicine Location Clinical Research Building, Room 1481A

Training Required Community based participatory research, Cancer and Health Disparities Access Open

Contact the

Core


Computational Cores

Bioinformatics and Data Mining Services

High Performance Computing (HPC)

Software Engineering


BIOINFORMATICS AND DATA MINING SERVICES What we can do for you

§ Consulting (free) – Small scale analysis requiring a maximum of four hours to complete § Basic Data Analysis – Analysis of basic data sets using commonly utilized bioinformatics software tools. § Advanced Data Analysis – Analysis of more complex data sets or more advanced analysis of basic data

sets. Includes the use of highly specialized bioinformatics software tools.

Staff

§ Nicholas Tsinoremas, Ph.D., Center Director § Mitsunori Ogihara, Ph.D., Data Mining Program Director § Enrico Capobianco, Ph.D., Lead Bioinformatics Scientist § Zhijie Jiang, Ph.D., Associate Scientist § Daria Salyakina, Ph.D., Assistant Scientist § Camilo Valdes, Senior Bioinformatics Research Analyst

Core Director

Enrique Capobianco, Ph.D.

Core Manager Evelyn Cruz Contact [email protected] / (305) 243-‐4962

Campus/Department Coral Gables Campus, Center for Computational Science Location Gables One Tower, Suite 600, 1320 S Dixie Hwy, Miami, FL 33146

Training Required Inquire Access Open

Contact the

Core


HIGH PERFORMANCE COMPUTING SERVICES


§ Systems administration and consulting – Consulting for initial setup of compute systems purchased by end user.

§ Advanced HPC systems administration -‐ Initial set up of systems requiring advanced or specialized OS load, software packages, etc., for systems purchased by end user.

§ Storage implementation – Initial set up of cloud storage on existing HPC equipment. This requires purchase of storage expansion unit.

§ HPC node services – Initial set up of compute time on existing CCS systems. § Cloud Storage Maintenance – Yearly (ongoing) administration fee for maintenance of longer-‐term storage

on previously purchased storage expansion units. § Systems Maintenance – Continuous, annual support per server/node for compute systems purchased by

end user. § HPC node compute time on Pegasus – Dedicated compute time on Pegasus.Systems hosting – Facilities

and power for housing systems at the NAP for systems purchased by end user.

Instrumentation

§ Pegasus – CentOS 6.5 based batch/interactive compute cluster § Jabberwocky – CentOS 6.2 based interactive visualization cluster § Elysium – CentOS 6.2 based secure data processing cluster (HIPAA/IRB compliant) § DAVID (Distributed Access for Visualization and interaction with data) Cloud

Core Director

Joel Zysman, Ph.D.



Training Required Training modules available on the CCS website: ccs.miami.edu/hpc. Live training sessions offered during the academic year, visit site for details.

Access Open

Contact the

Core


SOFTWARE ENGINEERING GROUP

What we can do for you The CCS Software Engineering group is a team of professional software engineers who work together using established software engineering practices, including following accepted and documented coding standards and conducting code reviews. Technologies include, primarily. Java, but also C++ and PHP expertise, Oracle/MySQL/PostgreSQL relational DBs, OWL/Jena-‐Semantic Web App development, JavaScript-‐AJAX-‐enabled UI development, Lucene-‐Text, search/mining, and Mule/Mirth for message-‐based systems.

§ Consulting Services -‐ Investigating and advising collaborators regarding technologies available for application to their specific areas of interest.

§ Systems Design – Technical design of applications and architecting systems. § Systems Development – software development performed by a team of engineers on a project

basis.

Core Director

Chris Mader, Ph.D.



Training Required Inquire Access Open Co

ntact the

Core


Genomics Cores

Biorepository Core Facility, (HIHG)

cGMP Facility, (HIHG)

Genotyping Core Facility, (HIHG)

Gene Expression Core Facility, (HIHG)

Oncogenomics Core Facility, Sylvester Comprehensive Cancer Center

Sequencing Core Facility, (HIHG)


BIOREPOSITORY CORE FACILITY (HIHG) What we can do for you The CGT biorepository offers a wide-‐range of services and currently houses more than a million samples collected over the last 30 years. Biorepository scientists process, archive, and retrieve biological samples as a valued resource for genomic research. Extensive experience in the use of the Nautilus LIMS and barcode printing through with Brady LabelSoft8 software allows for personalized and secure solutions for sample storage and retrieval. With a wide variety of sample processing options including automated DNA extraction with the Qiagen Autopure LS, plasma isolation, creation of blood cards, DNA extraction from many sources, DNA quantitation and qualitation, whole genome amplification using the Qiagen Repli-‐G kit sample archiving, and cell-‐line lymphoblast immortalization and primary fibroblast tissue culture we offer sample solutions to suit any project’s customized needs.

§ DNA/RNA Extraction § Sample archiving, retrieval & allocation § Unique and custom labels printing § DNA/RNA quantitation & qualitation § Tissue culture § Whole genome amplification § Biospecime, biohazard shipping § Sample acquisition kits

Instrumentation

§ BioMek FX Liquid Handling Systems § Qiagen Autopure LS § Qiagen Qiasymphony § Agelinet Bioanalyzer § Brroks Automates SmaRTStore A3+ Sample Archiving System § NanoDrop 8000 Spectrophotometer § Qubit Fluorometer § Brady IP Label Printers

Center Core Director

John P. Hussman Institute for Human Genomics (HIHG) Patrice Whitehead

Contact [email protected] / (305) 243-‐5CGT Campus/Department Leonard M. Miller School of Medicine

Location Biomedical Research Building, 528 Training Required Inquire


Core


CGMP CELL PROCESSING FACILITY (DRI)

What we can do for you The cGMP core provides cell processing, storage and distribution:

§ Human pancreatic islet cells (allogeneic and autologous): isolation, culture and distribution clinical and research applications;

§ Islet product characterization assays; § Immunomodulating and helper cell productions (T-‐Reg Cells, MSCs, NK cells, endothelial cells, dendritic

cells): isolation/selection, culture & expansion, and short-‐and long-‐term storage; § Vertebral body and iliax crest marrow, and peripheral blood: processing, selection of targeted cell

populations (e.g. CD34+ cell using Clinimax), cryopreservation and short-‐ and long-‐term storage; § Cellular-‐based vaccine products: establishment of Master Cell Banks & Working Cell Banks, culture and

expansion, storage, and characterization for batch release; § Adult adipose stem cells: isolation, culture and characterization; § Trans-‐differentiation of various cell types; § Neuronal cell types (Schwann Cells): isolation, culture and expansion, characterization for lot release; § Cryopreservation, short-‐and long-‐term storage, thawing and preparation for distribution of human cell

types, for research and clinical applications; § Product characterization & analysis: ELISA, FACS, cell counts and viability assessment, Endotoxin testing; § Process development and scale-‐up operations for clinical applications to support Phase I/II clinical trials; § Development and validation of product characterization, analytical and QC assays, and stability studies; § Regulatory support: development of Standard Operating Procedures, QC/QA support, development of

regulatory strategy, FDA submissions and communication, IRB submissions and communication

Instrumentation

§ Biosafety cabinets, horizontal clean bench § Isolex instruments, Microscopes § Clinimacs instrument § Heat sealers, Control rate freezers, sterile docking device § Liquid nitrogen storage tanks, equipment unique to isolation of human islet cells.


Diabetes Research Institute Elina Linetsky, Ph.D.

Contact (305) 243-‐3517 / [email protected] Campus/Department Leonard M. Miller School of Medicine

Location Diabetes Research Institute (DRI), Room 4014 Training Required Inquire

Access Open

Contact the

Core


GENOTYPING CORE FACILITY (HIHG)

What we can do for you The CGT genotyping core features platforms spanning low to high throughout capacities that can be tailored to meet your study’s individual goals. We have extensive knowledge and experience on all Illumina, Affymetrix, Life Technologies Taqman and Open Array genotyping platforms. Whole Genome Genotyping and Copy Number Analysis. Whole Genome Genotyping and Copy Number Analysis

§ Illumina Whole Genome Genotyping Arrays § Affymetrix Human 6.0 Array

Custom Mid to High-‐Plex Genotyping

§ Illumina iselect Beadchips Custom Low to Mid-‐Plex Genotyping

§ Life Technologies Open Array § Life Technologies Taqman Allelic Discrimination Assays

Focused Genotyping (specialized content products)

§ Illumina Beadchips Epigenetics: Array based Methylation Analysis

§ Illumina Methylation 450K Array Instrumentation

§ Biosafety cabinets, horizontal clean bench § Isolex instruments, Microscopes § Clinimacs instrument § Heat sealers, Control rate freezers, sterile docking device § Liquid nitrogen storage tanks, equipment unique to isolation of human islet cells.


John P. Hussman Institute for Human Genomics (HIHG) Ioanna Konidari, Ph.D.

Contact (305) 243-‐5CGT / [email protected] Campus/Department Leonard M. Miller School of Medicine

Location Biomedical Research Building, Room 528 Training Required Inquire

Access Website

Closed High.med.miami.edu Co

ntact the

Core


GENE EXPRESSION CORE FACILITY (HIHG)

What we can do for you The CGT gene expression core utilizes Affymetrix GeneChip Arrays and Illumina BeadChips to enable researches to identify gene expression variation in single genes, targeted set of genes, or entire genomes. Our expertise across a variety of platforms allows us to execute experiments with consistency and accuracy. Instrumentation

§ Affymetrix GeneChip Scanner 300 § Affymetrix Fluidics Station 450 § Illumina iScan System § Illumina BeadArray Readers § Roche Lightcycler LC 480 § Eppendorf epMotion 5075 § Agilent 2100 Bioanalyzers


John P. Hussman Institute for Human Genomics (HIHG) William Hulme, Ph.D.

Contact (305) 243-‐5CGT / [email protected] Campus/Department Leonard M. Miller School of Medicine

Location Biomedical Research Building, 627 Training Required None

Access Closed

Contact the

Core


ONCOGENOMICS CORE FACILITY

What we can do for you The Oncogenomics Core Facility provides researchers with access to the latest technology and chemistries used for the molecular analysis of DNA and RNA. This shared resource also provides investigators with the needed expertise for the detection, quantification, and characterization of genes and gene products.

§ DNA and RNA extraction § NanoString gene expression/CNV assays § Illumina gene expression microarrays § Exiqon miRNA qPCR § qPCR and digital droplet PCR § Illumina Next-‐Generation Sequencing (NGS)

Instrumentation

§ Agilent 2100 Bioanalyzer § NanoDrop 8000 § Qubit 3.0 Fluorometer § NanoString nCounter HS analysis system § Illumina iScan microarray scanner § Illumina NextSeq500 Sequencer § Raindance Raindrop digital droplet PCR § Two Roche Lightcycler LC480 real-‐time PCR machines

Core Director Siôn Ll. Williams, Ph.D. Academic Director Ramin Shiekhattat, Ph.D.

Contact (305) 243-‐7927 / [email protected] Campus/Department Leonard M. Miller School of Medicine,

Sylvester Comprehensive Cancer Center Location Biomedical Research Building, 542C

Training Required OCF is a fee-‐for-‐service limited access core that does not grant investigators access to any instrumentation. All samples are handled, processed and analyzed by OCF staff.

Access Open core that accepts samples from any investigator Contact the

Core


SEQUENCING CORE FACILITY (HIHG) What we can do for you The CGT sequencing core offers a wide range of services utilizing the Illumina HiSeq/NextSeq/MiSeq platforms, as well as the Lifetechnologies PGM and 3730xl platforms.

§ Whole Exome / Custom Capture § Whole Genome Sequencing § RNA Sequencing § De novo Sequencing § Microbiome / Metagenomics § Sanger Sequencing § Epigenomics

Instrumentation

§ Illumina HiSeq 3000 § Illumina HiSeq 2500 § Illumina NextSeq § Illumina MiSeq § Life Technilogies PGM § Life Technologies 3730xl § Lifetechnologies 3130xl

§ Perkin Elmer Sciclones § Perkin Elmer Zephyr § Perkin Elmer GX § Eppendorf epMotion 5075 § Agilent 2100 Bioanalyzers § Roche Lightcycler LC 480 § Covaris S2 Ultra-‐Sonicator


John P. Hussman Institute for Human Genomics (HIHG) William Hulme, Ph.D.

Academic Director Ionna Konidari, Ph.D. Contact (305) 243-‐5CGT / [email protected]

Campus/Department Leonard M. Miller School of Medicine Location Biomedical Research Building, 627

Training Required Inquire Access Open Co

ntact the

Core


Imaging Cores

Advanced Microscopy

Analytical Imaging Core Facility

Confocal Microscopy / Molecular Core Lab

Neuroimaging Facility


CENTER FOR ADVANCED MICROSCOPY (UMCAM) What we can do for you

§ SEM Services § XL30 High Resolution SEM for Geological, Biological, Chemical and Material Science Applications § EDS (Energy Dispersive Spectroscopy) for elemental Analysis Characterization § Consultation on applications requiring fixation and complex preparation methodologies § Facility can accommodate UM as well as outside the university users

Instrumentation

§ FEI XL-‐30 SEM § EDS System for semi-‐quantification of elements above

atomic number 9 § Cressington Plasma Sputter Coater (routinely coat with Pd

or Au) § Digital Imaging

Core Co-‐Directors Francisco Raymo, Ph.D. and Roger LeBlanc, Ph.D. Core Manager Pat Blackwelder, Ph.D.

Contact (305) 775-‐5801 / [email protected] Campus/Department Coral Gables Campus

Location Knight Physics Building, 142a (Chemistry Nanoscience Annex) Training Required Use requires trained help. SEM class (MGG583) offered in the Spring.

Access Open

Contact the

Core


ANALYTICAL IMAGING CORE FACILITY What we can do for you

The Analytical Imaging Core Facility (AICF) is a joint core between the Diabetes Research Institute/ Sylvester Comprehensive Cancer Center and supports the development and use of novel imaging and analytical approaches to advance scientific research. It provides researchers with access to costly state-‐of-‐the-‐art analytical and imaging techniques for cellular and tissue imaging as well as molecular analysis of pathology specimens.

§ Wide field microscopy, including fluorescence and HE § Confocal microscopy, using modern Leica HyD detectors (very sensitive!) § Image processing for publications § Stop counting cells manually. We will design an automated protocol for you. § Image quantifications § Whole animal microscopy § Microdissection on slides or membranes

Instrumentation

§ Leica SP5 inverted confocal microscope, 5 lasers, high resolution and fast resonance scanners

§ Leica SP5 upright confocal, 5 lasers, MP § Leica LMD laser microdissection § Zeiss fluorescence microscope, b/y sensitive camera (CCD-‐60) § Leica DMIRB, color camera

Core Director Armando Mendez, Ph.D. Core Manager

Contact Marcia Boulina, Ph.D. (305) 243-‐8436 / [email protected]

Campus/Department Leonard M. Miller School of Medicine, Diabetes Research Institute/ Sylvester Comprehensive Cancer Center

Location Diabetes Research Institute (DRI), Room 6025, 1450 NW 10th Avenue Training Required Training provided at no additional cost (you pay instrument time only)

Access Open

Contact the

Core


CONFOCAL MICROSCOPY CORE/MOLECULAR CORE LAB


§ Training and use of the Biology Departments confocal microscope § Administration of and training on molecular core lab equipment § Sequencing of DNA samples

Instrumentation

§ Leica SP5 confocal microscope § Licor western blot imager § 3130 ABI DNA sequencer § Quantitative PCR machine (realtime) § Biorad imager

Core Director James Baker, Ph.D. Contact (305) 284-‐9055 / [email protected]

Campus/Department Coral Gables Campus Location Neuroscience Cox Annex, 36 (Molecular Core),

Neuroscience Cox Annex 223 (Confocal Microscopy Core) Training Required Yes

Access Open

Contact the

Core


IMAGING AND HISTOLOGY CORE What we can do for you The Imaging/Histology Core supports the care and use of instrumentation for imaging of live and preserved organs, cells, tissues, as well as plates and arrays. This Core also provides computer software for the processing and quantification of image features. The core is comprised of four different facilities: Confocal Microscopy, Wide-‐field Microscopy, Stereo Microscopy, and Gel Imaging Systems.

§ Confocal Microscopy: Leica TCS SP5 Confocal; Zeiss LSM 700 Confocal

§ Wide-‐field Microscopy: Carl Zeiss inverted microscope (Axiovert 200m) with Zeiss MRm camera; Carl Zeiss Imager.Z1 with CoolSnap DS camera; Olympus IX50 inverted cell culture scope with Retiga camera; Axiostar Plus Upright Fluorescence Microscope

§ Stereo Microscopy: Zeiss Stemi SV11 Fluorescence Stereo Microscope

§ Gel Imaging Systems: GE imageQuant LAS4000 imaging station, FujiFilm LAS4000 imaging station, and GE

Typhoon trio scanner Histology Lab Equipment

§ ATP™ Tissue Processor (# ATP1-‐120, Triangle Biomedical Sciences, Inc.) § 2 Microtome Cryostats (International Equipment Company – Minotome) § Leica Jung knife sharpener § 2 micro optics Microtomy (Leitz #1512) § Spencer binocular microscope (AO #926963) § Lancer Vibratome 1000 and Vibratome 1000 Plus § Illuminated Tissue Flotation Bath (# 80086-‐990, VWR) § Paraffin Dispenser (# PD-‐120, Triangle Biomedical Sciences, Inc.)

Core Co-‐Directors Valery Shestopalov and Victor Perez-‐Quiniones Imaging Core Manager Gabriel Gaidosh / [email protected] Histology Technician Magda Celdran / [email protected]

Contact (305) 326-‐6048 Campus/Department Leonard M. Miller School of Medicine, Bascom Palmer Eye Institute

Location McKnight Vision Research Center, 4th and 7th Floors Training Required Yes, proficiency required before use of instrumentation

Access Open

Contact the

Core


NEUROIMAGING FACILITY


§ Provide time to conduct functional and structural magnetic resonance imaging (MRI) research studies

§ Provide access to physicist to set up MRI protocols § Provide MRI technologist to assist with data collection § Provide equipment necessary to conduct MRI research studies § Provide a DVD of the MRI images acquired during data collection

Instrumentation

§ General Electric MR750 3T MRI scanner § 32-‐channel and 8-‐channel head coils § Projection system § Eprime presentation computer § MRI-‐compatible response devices § Biopac Physiological recording § Resonance Technology eye-‐tracking § Mock Scanner § Motion Tracking System § Other equipment may become available. Please consult for full list and descriptions.

Core Director Jennifer Britton, Ph.D.

Core Manager Melyza Casanova Contact [email protected] / (305) 284-‐6082

Campus/Department Coral Gables Campus Location Neuroscience Cox Annex, Rooms 102, 104

Training Required MRI safety and equipment training required Access Closed

Contact the

Core


Marine Operations

Marine Operations Department

Rosenstiel School of Marine & Atmospheric Science 4600 Rickenbacker Causeway

Miami, FL 33149 (305) 421-‐4832 rsmas.miami.edu


RSMAS MARINE OPERATIONS What we can do for you

The RSMAS Marine Operations Department is responsible for the operation, maintenance and support of the F.G. Walton Smith, an advanced research catamaran designed for tropical oceanography. This vessel is operated as part of the University National Laboratory System (UNOLS).

Instrumentation Research Vessel the F.G. Walton Smith The Rosenstiel School’s primary research vessel is the F.G. Walton Smith. The state-‐of-‐the-‐art 96-‐foot-‐long catamaran is capable of reaching speeds of over 10 knots and has a draft of only 7 feet. This shallow draft enables it to explore inaccessible areas such as reefs, mangroves, grassbeds, and other shallow environments. The vessel accommodates 20 people in its ten two-‐person staterooms and encompasses 800 square feet of laboratory space, as well as an additional 800 square feet of multi-‐use space astern. Includes: Hawboldt Oceanographic Winches; Conductivity Temperature Depth Instrument; Water Sampling (Niskin) Bottles; Rescue Boat; Flo Thru Water Sampling System; Acoustic Doppler Current Profiler. RSMAS Small Boats

§ 15’ Boston Whaler/Outboard/Trailer (2) § 15’ Safeboat/Outboard/Trailer § 26’ Bluewater/Outboard/Trailer § 24’ Hydrasport/Outboard/Trailer § 18’ Hydrasport/Outboard/Trailer § 23’ Sea Cat/Outboard/Trailer

Required: Small Boat Certification of Training, check out with RSMAS Small Boats Manager

RSMAS Motor Pool Triple Axle Trailer; 2 & 4 Passenger Electric Carts; Freightliner Sprinter Van; F-‐350 Flatbed Truck; F350 HD 4 Wheel Drive Pickup; Ranger XLT Pickup; 15 Passenger Van Required: UM Drivers clearance and certification

Core Director RADM Richard R. Behn, Ph.D., NOAA (ret.) Contact [email protected] / (305) 421-‐4832

Campus/Department Rosenstiel School of Marine & Atmospheric Science / Marine Department Location McKnight, 4th and 7th Floors

Training Required MRI safety and equipment training Access Closed


IV. Emergency Management

The Office of Emergency Management (OEM) is responsible for coordinating the University’s preparation, response and recovery of any major emergency. Emergency numbers are printed on the back of all university-‐issued campus ID cards and badges.

§ Access the University of Miami Emergency Guide at www.miami.edu/mobile/emergency, specific action guidelines, important phone numbers and websites.

§ The University of Miami Emergency Notification Network (ENN) quickly disseminates urgent

messages. Visit the ENN website to sign-‐up for alerts. Download the University of Miami Emergency Guide or mobile app at www.miami.edu/mobile/emergency.

§ In case of a medical emergency, contact 911 or go to an emergency room, for non-‐emergency

medical issues contact the UM Health Clinic or your primary care provider.

Hurricane Preparedness for your Core The hurricane season runs from June 1 to November 30. Visit the Ready South Florida website at readysouthflorida.org for information on how to stay informed, develop your own evacuation plan and build a disaster preparedness kit. Please make sure your core is hurricane ready. You can find disaster preparedness checklists and information on ordering supplies at: http://research.med.miami.edu/discovery-‐research/discovery-‐preparedness.

IV

IMPORTANT EMERGENCY PHONE NUMBERS @ UM

Life Threatening Emergency 911 Emergency Information Hotline (800) 227-‐0354 Emergency Management & Disaster Planning (305) 243-‐9466 Emergency (305) 243-‐6000 UM Non-‐emergency (305) 243-‐7233 UM Rumor Control (305) 243-‐6079 UMMSOM Campus Security (305) 243-‐7233 University Police Department Coral Gables Campus (305) 284-‐6666 Department of Security Leonard M. Miller School of Medicine Campus

(305) 243-‐6000

Rosenstiel School of Marine & Atmospheric Science Campus Safety

(305) 421-‐4766 (305) 710-‐7991

Report Suspicious Activity (State-‐Wide) (855) 352-‐7233


V. Research Resources at the University of Miami

LIBRARIES The libraries of the University of Miami rank among the top research libraries in North America with a combined collection of over 3.2 million volumes, 74,000 current electronic and print serials. You will find libraries at all three campuses: Coral Gables, Rosenstiel, and Medical campuses.

Leonard M. Miller School of Medicine Louis Calder Memorial Library 1601 NW 10th Avenue Miami, FL 33136 Telephone: (305) 243-‐6403 http://calder.med.miami.edu General Reference Desk Telephone: (305) 243-‐6648 Email: [email protected]

University of Miami Main Library Otto G. Richter Library 1300 Memorial Drive Coral Gables, FL 33146 Telephone: (305) 284-‐3233 http://library.miami.edu Richter Reference Desk Telephone: (305) 284-‐4722 Email: [email protected]

OFFICE OF RESEARCH The Office of Research at the University of Miami provides an integrated network of administrative support and educational opportunities to facilitate scholarly activity, scientific discovery, and the responsible conduct of research. The Office of Research serves all University of Miami campus sites, including Coral Gables, the Leonard M. Miller School of Medicine, the Rosenstiel School of School of Marine and Atmospheric Science, and others.

ENVIRONMENTAL HEALTH AND SAFETY, RADIATION SAFETY, AND ANIMAL

WELFARE The Office of Environmental Health and Safety helps the University continuously improve its compliance with health, safety, and environmental regulations. The office provides support and training in an effort to avoid occupational, biological, and chemical hazards.

Contact information: Telephone: (305) 243-‐3400; Email: [email protected] Website: www.miami.edu/finance/index.php/environmental_health_safety/

Human Use Radiation Safety Committee The Division of Radiation Control ensures that the University of Miami and the Public Health Trust are in compliance with all regulations regarding the use of radioactive materials and radiation producing devices. Additionally, the division assures that these materials and devices are used in a manner that minimizes the radiation dose to employees, patients, and members of the general public.

Contact information: Telephone: (305) 243-‐6369; Email: [email protected] Website: facilities.med.miami.edu/divisions/radiation-‐cont

The Institutional Animal Care and Use Committee (IACUC) is a federally mandated university committee that ensures that the care and use of animals is appropriate and humane in accordance with animal welfare regulations. The committee reviews and approves animal use protocols; trains investigators and staff; inspects all animal facilities at the university; monitors animal research project to ensure compliance; and investigates concerns raised by faculty and staff regarding care and use of laboratory animals.

Contact information: Telephone: (305) 243-‐2311; Email: [email protected] Website: uresearch.miami.edu/iacuc

HUMAN SUBJECT RESEARCH OFFICE

The Human Subject Research Office (HSRO) provides administrative support for the University of Miami institutional review boards (IRBs). An IRB is a group of individuals charged with reviewing proposed research involving human subjects to ensure protection of those subjects.

Contact information: Telephone: (305) 243-‐1790; Fax: (305) 243-‐3328 Website: http://uresearch.miami.edu


INTELLECTUAL PROPERTY AND LICENSING

The U Innovation office is the home of technology advancement at the University of Miami. The office is comprised of the Office of Technology Transfer (Intellectual Property Strategy and Licensing) and the Wallace H. Coulter Center for Translational Research. The Office of Technology Transfer plays a major role in protecting and preserving the intellectual property assets of the university and offers education and training for researchers on technology advancement, patents and licensing.

Contact information: Telephone: (305) 243-‐5689; Email: [email protected] Website: www.miami.edu/index.php/u_innovation/

RESEARCH LISTSERVS The Office of Research’s listservs are the primary communication tool for the research community. The listservs are resources you can use to leverage the collective knowledge of the University to help you solve problems and improve the effectiveness of your research operations:

• Research Listserv: Read about new funding opportunities and updates to policies and procedures from external funding agencies and the University. You may also post questions, and find collaborators and specialized resources.

• Research Administrators Listserv: Read about new funding opportunities and updates to policies and procedures from external funding agencies and the University. You may also post questions and connect with other research administrators.

• Clinical Research Listserv: Join this listserv for human subjects’ researchers to learn about new policies, training and education opportunities, and process changes from the University. Share information on clinical research, and find collaborators and specialized resources.

• International Research Listserv: This listserv targets University faculty, staff, and students engaged in international research and permits subscribers to post questions and share information on topics of interest related to international research Contact information Website: http://uresearch.miami.edu / Telephone: (305) 673-‐7300

If you have any questions, comments, or suggestions contact Dr. Karin Scarpinato.

University of Miami