Behavioral Health and Survey Research Core*


The Behavioral Health and Survey Research Core (BHSRC) is a developing shared resource designed to support Duke Cancer Institute (DCI) investigators interested in using state-of-the-science, evidence-based behavioral and epidemiological research methods for cancer-related research. The BHSRC is led by Drs. Kathryn Pollak and Laura Fish who together have over 30 years of combined experience designing and implementing surveys and developing educational materials. Ms. Katherine Zeph has over 25 years of experience as a graphic designer. Collectively, BHSRC staff provides unique expertise in behavioral science, epidemiology, and survey research.

Kathryn Pollak, PhD

Director

Kathryn Pollak, PhD

kathryn.pollak@duke.edu
919.681.4757

Email Me!

In our first year as a developing shared resource, we have already helped 20 investigators from four of the DCI programs develop surveys, conduct formative work to answer preliminary questions (e.g., how do patients with AML understand their diagnosis and treatment options?), and develop patient materials. We feel now investigators are not limited in the research questions they can ask as they can use the BHSRC.



In our first year as a developing shared resource, we have already helped 20 investigators from four of the DCI programs develop surveys, conduct formative work to answer preliminary questions (e.g., how do patients with AML understand their diagnosis and treatment options?), and develop patient materials. We feel now investigators are not limited in the research questions they can ask as they can use the BHSRC.

Kathryn Pollak, PhD

Director

Kathryn Pollak, PhD

kathryn.pollak@duke.edu
919.681.4757

Email Me!

Services


  • Manage and implement all aspects of needs assessment research, including developing interview guides, facilitating focus groups and structured interviews, coding and analyzing qualitative data
  • Design surveys that patients can understand and that will provide valid data (e.g., using right measures and asking in the correct order)
  • Develop materials to convey information to patients in a way that is understandable and matches their literacy and numeracy levels

Leadership and Contact


Kathryn Pollak, PhD

Director
919.681.4757
Kathryn.pollak@duke.edu

Kathryn Pollak, PhD

Kathryn.pollak@duke.edu
919.681.4757

Email Me!

Laura Fish, PhD

Assistant Director
919.681.3820
laura.fish@duke.edu

Laura Fish, PhD

laura.fish@duke.edu
919.681.3820

Email Me!

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Katherine Zeph

Project Manager and Graphic Designer
919.668.7492
katherine.zeph@duke.edu

Katherine Zeph

katherine.zeph@duke.edu
919.668.7492

Email Me!

Bioinformatics


The Bioinformatics Shared Resource supports the bioinformatics research needs of DCI investigators, including their needs for complex genomic data management, data integration, computing and statistical analysis. Its mission is to provide a high-quality, service-oriented, coordinated and cost efficient bioinformatics infrastructure for DCI researchers, which increases collaborations across DCI programs, other Duke programs, and external investigators. The Bioinformatics Shared Resource covers every facet of analysis of high-dimensional genomic data, from the design stage, to preprocessing (background, normalization and summarization of RNA microarrays; genotype and copy number calling from genome-wide association study [GWAS] platforms; and alignment, normalization (RNA-seq) and SNV calling (DNA-seq) of next-generation sequencing [NGS] platforms), to high-level association analyses with complex phenotypes, and genomic annotation of results. In cases where off-the-shelf methods and software tools cannot address the scientific question at hand in a rigorous manner, the shared resource staff, using its expertise in applied and theoretical statistics and computing, is able to offer customized solutions to DCI investigators. Currently, these services are available to DCI members at no charge.

Kouros Owzar, PhD

Director

Kouros Owzar, PhD

kouros.owzar@duke.edu
919.681.1829

Email Me!

Our shared resource provides research support to DCI investigators for the design, management, and analysis of genomics data from genomic assays, including microarrays, GWAS, RNA-Seq, DNA-seq, and proteomics. Our emphasis is on adherence to sound statistical principles and to the conduct of reproducible analysis. Lack of appropriate and adequate statistical methodology and computational tools should not limit the scope of scientific discovery and rigor.



Our shared resource provides research support to DCI investigators for the design, management, and analysis of genomics data from genomic assays, including microarrays, GWAS, RNA-Seq, DNA-seq, and proteomics. Our emphasis is on adherence to sound statistical principles and to the conduct of reproducible analysis. Lack of appropriate and adequate statistical methodology and computational tools should not limit the scope of scientific discovery and rigor.

Kouros Owzar, PhD

Director

Kouros Owzar, PhD

kouros.owzar@duke.edu
919.681.1829

Email Me!

Services


  • Pre-processing, analysis, and annotation of molecular assays including microarray, GWAS, RNA-seq, DNA-seq, Chip-seq, and flow cytometry platforms
  • Manuscript writing and review
  • Grant writing support
  • Provision of rigorous genomic study designs (including power and sample size calculations using simulation techniques)
  • Provision of turnkey computing solutions for routine analyses

Equipment and Technology


  • Hardware owned and managed by the Bioinformatics shared resource:
  • 64 core Opteron server with 512GB of RAM
  • 32 core Opteron server with 128GB of RAM
  • 48TB of local storage (twenty-four 4TB drives in RAID 10)
  • Quadro K6000 GPU (2880 streaming cores and 12GB of memory)
  • Quadro 2000 GPU (192 streaming cores and 1GB of memory)
  • High-performance computing (HPC) clusters managed by Duke University:
  • Duke Shared Cluster Resource (DSCR) CPU Cluster providing 5220 cores distributed over 458 nodes and eleven M2070 Tesla GPU cards
  • Blue Devil GPU Cluster consisting of GT2000, GTX275 and Tesla C1060 cards
  • Forty nodes, each with 16 CPU-cores and either 128 GB or 256 GB of RAM currently providing 530TB of NetApp E-series storage using the IBM General Parallel File System (GPFS)
  • Storage Nodes:
  • Isilon servers managed by OIT and DHTS
  • Amazon Glacier storage (AWS)

Leadership and Contact


 

Kouros Owzar, PhD

Director
919.681.1829
kouros.owzar@duke.edu

Kouros Owzar, PhD

kouros.owzar@duke.edu
919.681.1829

Email Me!

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Location

  • Duke Box, 2721, 2424 Erwin Road, Suite 1102, 11074 Hock Plaza, Durham, NC 27705
Click Here To Visit The Bioinformatics Website

Biostatistics


The Biostatistics Shared Resource (BSR) provides access to state-of-the-art expertise in biostatistics methods for study design, analysis, and reporting. The BSR has embedded Masters and Doctoral level biostatisticians in each of the 12 disease-site groups as well as Cancer Control and Population Science to provide ongoing assistance and collaboration in the development of research, grant applications, and clinical protocols from concept, active trial operations to publications of study outcomes and results. While initially focused on translational research and clinical trials, this resource is extending its partnership activities into other cancer research areas, such as health services research, observational studies, epidemiology, basic sciences, and others to meet the needs of the DCI. The BSR participates in and co-leads the development and testing of appropriate systems for trial data management and linkages through Medidata Rave, Medidata Balance, RedCap, and other tools. It also provides assistance with clinical trial compliance, reporting, oversight and provides scientific review of all DCI protocols.

Terry Hyslop, PhD

Director

Terry Hyslop, PhD

terry.hyslop@duke.edu
919.681.5047

Email Me!

People come to us from all over the DCI with promising new research areas or ideas. We work to make that research the best it can be. That means a lot of thinking, designing, analyzing and thinking again during all stages of research.



People come to us from all over the DCI with promising new research areas or ideas. We work to make that research the best it can be. That means a lot of thinking, designing, analyzing and thinking again during all stages of research.

Terry Hyslop, PhD

Director

Terry Hyslop, PhD

terry.hyslop@duke.edu
919.681.5047

Email Me!

Services


  • Access to state-of-the-art expertise in biostatistics methods for study design, analysis, and reporting
  • Partnerships in disease-specific clusters with embedded biostatistics teams providing ongoing development of research, grant applications, and clinical protocols
  • Participation and co-leadership in the development and testing of appropriate systems for trial data management and linkages through Medidata Rave, Medidata Balance, RedCap, and other tools
  • Assistance with compliance of clinical protocols through support of clinicaltrials.gov reporting, preparation of DSMB summaries, and participation in the DSMC meetings
  • Scientific review of all DCI protocols, service on the Cancer Protocol Committee (CPC) and the Safety Oversight Committee (SOC)

Equipment and Technology


  • Hardware owned and managed by the Bioinformatics Shared Resource: ◦64 core Opteron server with 512GB of RAM
  • 64 core Opteron server with 512GB of RAM
  • 32 core Opteron server with 128GB of RAM
  • 48TB of local storage (twenty-four 4TB drives in RAID 10)
  • Quadro K6000 GPU (2880 streaming cores and 12GB of memory)
  • Quadro 2000 GPU (192 cores and 1GB of memory)
  • HPC clusters managed by Duke University
  • Duke Shared Cluster Resource (DSCR) CPU Cluster providing 5220 cores distributed over 458 nodes and eleven M2070 Tesla GPU cards
  • Blue Devil GPU cluster consisting of GT2000, GTX275 and Tesla C1060 cards
  • Forty nodes, each with 16 CPU-cores and either 128 GB or 256 GB of RAM currently providing 530TB of NetApp E-series storage using the IBM General Parallel File System (GPFS)
  • Storage Nodes
  • IGSP Netapp SAS, Netapp SATA and Dell SATA drive storage
  • Amazon Glacier storage (AWS)

Leadership and Contact


 

Terry Hyslop, PhD

Director
919.681.5047
terry.hyslop@duke.edu

Terry Hyslop, PhD

terry.hyslop@duke.edu
919.681.5047

Email Me!

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Location

  • 2424 Erwin Road, 8037 Hock Plaza, Durham NC 27705
Click Here To Visit The Biostatistics Website

Biospecimen Repository and Processing Core


The Biospecimen Repository and Processing Core/Shared Resource (BRPC) provides investigators fresh, frozen, or paraffin-embedded solid tissue samples, extracted DNA/RNA, serum, plasma, and PBMC DNA necessary for their research. The BRPC functions with IRB approval and obtains informed consent of patients willing to donate tissue samples to research. Patients may consent to donate “excess tissue” from surgical events as well as “additional tissue” (paired needle core breast biopsies, for example) along with blood samples. The BRPC functions under the favored “honest-broker” model of biobanking. The director of the BRPC is a pathologist responsible for maximizing patient tissue available for research while ensuring that sufficient, intact tissue is available for clinical diagnostic assessment and reporting. Governance of biospecimens is provided by multidisciplinary disease group leadership rather than BRPC itself.

Shannon J. McCall, MD

Director

Shannon J. McCall, MD

shannon.mccall@dm.duke.edu
919.684.2531

Email Me!

Tissue donated to the BRPC makes a huge, lifesaving impact, both for furthering our understanding of cancer and impacting the future of patient care. These research samples are a huge resource for clinical trials and laboratory investigations throughout the DCI.



Tissue donated to the BRPC makes a huge, lifesaving impact, both for furthering our understanding of cancer and impacting the future of patient care. These research samples are a huge resource for clinical trials and laboratory investigations throughout the DCI.

Shannon J. McCall, MD

Director

Shannon J. McCall, MD

shannon.mccall@dm.duke.edu
919.684.2531

Email Me!

Services


  • Full-service biobanking from informed consent to nucleic acid extraction
  • Serves the biobanking needs of Disease-Site groups of the DCI
  • Consultation on new protocols involving tissue
  • Cost-effective and rapid access to de-identified tissues for proof-of-concept studies
  • Complete integration with Surgical Pathology at Duke

Equipment


  • Cryogenic storage: Liquid nitrogen storage tank (one), −80ºC freezers (five)
  • Sensaphone Remote Temperature Monitoring System of 161 ft3 of cryogenic storage space
  • Histology: Paraffin tissue processor, embedding station
  • Nucleic Acid Quality assurance: NanoDrop® ND-1000, gel documentation system
  • Specimen Identity: barcode printers, paraffin block printers and barcode readers
  • Archiving: Digital photomicrograph station, paraffin and slide storage system
  • Safety: Biosafety cabinet, flammables storage

Leadership and Contact


 

Shannon J. McCall, MD

Director
919.684.2531
shannon.mccall@dm.duke.edu

Shannon J. McCall, MD

shannon.mccall@dm.duke.edu
919.684.2531

Email Me!

Melissa Flowers

Senior Laboratory Administrator
919.684.6928
melissa.flowers@duke.edu

Melissa Flowers

melissa.flowers@duke.edu
919.684.6928

Email Me!

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Cancer Center Isolation Facility


The Cancer Center Isolation Facility (CCIF) provides the physical plant and supports work with hazardous materials at biosafety level 2, recombinant DNA, chemotherapeutics, as well as the maintenance of immunosuppressed and specific pathogen free rodents. Immunocompromised mice (outbred athymic nude mice and inbred Nod SCID gamma (NSG) mice) are produced at a reduced cost for Cancer Institute members and are available to all investigators at Duke who have an approved IACUC animal protocol. The CCIF also maintains numerous xenograft lines derived from both pediatric and adult primary and metastatic tumors, including various brain tumors, sarcomas, melanomas, and breast cancers. CCIF personnel advise or suggest mentors to DCI investigators who require assistance with breeding services, veterinary or diagnostic services, animal and experimental protocol development, inoculation or testing of cell lines, preferable location of such inoculations, and a large variety of other information pertinent to performing safe and efficient research in the investigation of cancer biology. CCIF contains facilities for the conduct of efficacy and toxicity studies that meet Good Laboratory Practice (GLP) regulations as required by the Food and Drug Administration to obtain Investigational New Drug permits.

Darell Bigner, MD, PhD

Scientific Coordinator

Darell Bigner, MD, PhD

bigne001@mc.duke.edu
919.684.5018

Email Me!

The Cancer Center Isolation Facility is one of the oldest DCI Shared Resources, having provided containment for specialized laboratory operations and housing for immunosuppressed and transgenic animals. The per diem charges are partially subsidized by the Cancer Center Support Grant.



The Cancer Center Isolation Facility is one of the oldest DCI Shared Resources, having provided containment for specialized laboratory operations and housing for immunosuppressed and transgenic animals. The per diem charges are partially subsidized by the Cancer Center Support Grant.

Darell Bigner, MD, PhD

Scientific Coordinator

Darell Bigner, MD, PhD

bigne001@mc.duke.edu
919.684.5018

Email Me!

Services


  • Veterinary services
  • Diagnostic services
  • Husbandry services
  • Athymic mouse and Nod SCID gamma (NSG) breeding colonies
  • Animal or experimental protocol consults, including the provision of technical services

Equipment and Technology


  • 33 laboratories for animal holding/research purposes
  • ABSL-2/Hazardous chemical containment capability
  • Collaborative environment dedicated to cancer research
  • State of the art Individually Ventilated Cage (IVC) housing racks for barrier or containment housing
  • Automatic animal watering system, which includes a reverse osmosis filtration system
  • In Vivo Optical Animal Imaging available

Leadership and Contact


John Norton, DVM, PhD

Director
919.684.4204
john.norton@duke.edu

John Norton, DVM, PhD

john.norton@duke.edu
919.684.4204

Email Me!

Darell Bigner, MD, PhD

Scientific Coordinator
919.684.5018
bigne001@mc.duke.edu

Darell Bigner, MD, PhD

bigne001@mc.duke.edu
919.684.5018

Email Me!

Francis Sun, DVM

Associate Director of DLAR
919.684.2341
francis.sun@dm.duke.edu

Francis Sun, DVM

francis.sun@duke.edu
919.684.2341

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Keith St. Pierre, BA, RLATG, CMAR

Operations Manager
919.681.7440
keith.stpierre@duke.edu

Keith St. Pierre, BA, RLATG, CMAR

keith.stpierre@duke.edu
919.681.7440

Email Me!

Flow Cytometry


The Flow Cytometry Shared Resource (FCSR) operates, maintains, and upgrades instrumentation for flow cytometric analysis and cell sorting of cells prepared by investigators and brought to the FCSR. In addition to cell sorting, acquiring, analyzing, archiving, and preparing flow data for publication, the FSCR staff provides consultation, technical advice, collaboration, and maintains a library to disseminate technical information to potential users. The FCSR staff has experience in nearly all areas of flow cytometric analysis and cell sorting applications and has helped investigators develop a variety of new applications. Staff members recommend assays, help develop and troubleshoot new protocols, participate actively in data analysis, and, in general, work closely with investigators to fine tune their individual experiments. The FSCR operates three cell sorters, five cell analyzers, and an Amnis Imagestream MarkII image cytometer.

Michael Cook, PhD

Co-Director

Michael Cook, PhD

cook0016@dm.duke.edu
919.613.7818

Email Me!

We have to know something about the cell biology of each project, how our computers, lasers, and software work to get the maximum out of each measurement, and a little bit about human nature. We have nine instruments and four full time employees, as well as excellent business support from the Department of Immunology. Last year we served over 160 laboratories.



We have to know something about the cell biology of each project, how our computers, lasers, and software work to get the maximum out of each measurement, and a little bit about human nature. We have nine instruments and four full time employees, as well as excellent business support from the Department of Immunology. Last year we served over 160 laboratories.

Michael Cook, PhD

Co-Director

Michael Cook, PhD

cook0016@dm.duke.edu
919.613.7818

Email Me!

Services


  • Our staff performs all cell sorting. We also assist in acquiring, analyzing, archiving, and preparing flow data for client publications.
  • Staff provides training for self-users of the analyzers and image cytometer, and consultation, technical advice, collaboration, and technical information for potential users.
  • Staff members recommend assays, help to develop and troubleshoot new protocols, and participate actively in data analysis.
  • Our analyzers and image cytometer are available 24/7 to trained individuals. The FCSR staff has experience in nearly all areas of flow cytometric analysis and cell sorting applications and strives to help investigators develop new applications. In general, we work closely with investigators to fine tune their individual experiments.

Equipment and Technology


  • Cell Sorters
  • Beckman-Coulter (B-C) Astrios: Purchased in 2012, this is our most versatile cell sorter. It has four lasers (405 nm, 488 nm, 561 nm, and 640 nm). It can collect up to 14 fluorescence signals and is housed inside a Baker Bioprotect III tissue culture hood for increased biosafety. It can sort up to six populations simultaneously with index sorting to identify individual cells in single cell sorting mode. It is equipped with automatic sort setup and sort monitoring functions.
  • B-C MoFlo XDP (2014): It has four lasers (405 nm, 488 nm, 561 nm, and 640 nm). It can collect up to 14 fluorescence signals. The Legacy also features 4-way sorting, and automatic sort monitoring, and can sort 4 simultaneous populations.
  • BD DiVa: This sorter was purchased in 2002 as a joint venture between the DCI, the School of Medicine, and the Department of Immunology. It is equipped with a single cell deposition unit, a recirculating chiller, 4 way sorting and a biohazard control unit. It has three lasers for excitation, 488 nm, 360 nm UV or 413 in the violet, and a HeNe laser at 632 nm. It has 12 fluorescence detectors. It is currently our only cytometer with a UV laser.
  • Analyzers
  • Two identical BD Canto II instruments, one of which has a 96 well plate loader. They have three lasers and can measure eight fluorescence parameters. They are available 24/7.
  • A BD FACSCalibur (2 laser & 4 colors) in 307 Jones Bldg. and a BD FACScan (1 laser & 3 colors) in C316 LSRC.
  • Imagestream Mark II located in 369 Jones Bldg. This versatile instrument has four lasers. It stores several fluorescent images as well as a bright field image for each cell at 20, 40, or 60X magnification while running at 1,000 cells per second.
  • iMac workstation with FloJo10 (or 9) in 369 Jones Bldg.

Leadership and Contact


 

Michael Cook, PhD

Co-Director
919.613.7818
cook0016@dm.duke.edu

Michael Cook, PhD

for technical consultation
cook0016@dm.duke.edu
919.613.7818

Email Me!

Michael S. Krangel, PhD

919.684.4985
krang001@dm.duke.edu

Michael S. Krangel, PhD

krang001@dm.duke.edu
919.684.4985

Email Me!

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Locations

  • Rooms 306, 307, 336, 343, and 369 Edwin Jones Cancer Research Building , Durham, NC 27710
  • Room C316, Levine Science Research Center, Durham, NC 27710
Click Here To Visit The Flow Cytometry Website
Click Here For The Registration Form
Click Here For Online Scheduling
Help finding antibodies and fluorochromes

High Resolution NMR Spectroscopy


The High Resolution NMR Spectroscopy Shared Resource provides access to and technical support for state-of-the-art instrumentation essential for modern magnetic resonance spectroscopy, and links to the NMR Facility at the North Carolina Research Campus in Kannapolis, NC, which has one of only two 950MHz instruments in the United States. The Duke shared resource has gained a worldwide reputation for being active in the design and implementation of new methodologies in biological NMR and stable isotope labeling techniques, which are routinely used for molecular characterization to advance DCI members’ research. The expert staff train and assist users in both the fundamentals and the most modern and advanced applications of powerful NMR technologies.

Leonard Spicer, PhD

Director

Leonard Spicer, PhD

spicer@biochem.duke.edu
919.684.4327

Email Me!

The structure and function of RNA and DNA can be difficult to study because they’re very mobile molecules. They can be difficult to crystallize to examine by x-ray crystallography, and even then, the still images don’t tell the entire story of how these molecules function. The high-resolution NMR spectroscopy shared resource is uniquely suited to studying the structure and function of mobile molecules such as nucleic acids.
Hashim al-Hashimi, major user group director, Professor, Biochemistry and Chemistry



The structure and function of RNA and DNA can be difficult to study because they’re very mobile molecules. They can be difficult to crystallize to examine by x-ray crystallography, and even then, the still images don’t tell the entire story of how these molecules function. The high-resolution NMR spectroscopy shared resource is uniquely suited to studying the structure and function of mobile molecules such as nucleic acids.
Hashim al-Hashimi, major user group director, Professor, Biochemistry and Chemistry

Leonard Spicer, PhD

Director

Leonard Spicer, PhD

kathryn.pollak@duke.edu
919.681.4757

Email Me!

Services


  • Cost effective access to state-of-the-art NMR instrumentation
  • Expert training in the use of NMR instrumentation and methods
  • Assistance in planning and implementing experiments and in data analysis
  • On-site consultation and collaboration with two full time PhD level scientific staff members and an electronics engineer/instrument specialist who are all expert in advanced applications using these techniques for biochemical and biomedical research
  • Development of new methods and implementation of new techniques for acquiring and analyzing NMR data

Equipment and Technology

  • State-of-the-art ultra-high field 800MHz Varian/Agilent DirectDrive2 spectrometer fully configured with four RF channels, two receivers, and 1H/13C/15N cryogenic and room temperature triple probes with pulsed field gradients.
  • Recently installed Bruker Avance III 700MHz spectrometer with both liquids and solids capabilty fully configured for biomolecular studies with room temperature triple resonance probes. The liquids probe is capable of 19F detection with 1H decoupling and vise versa.
  • Bruker Avance III 700MHz spectrometer fully configured for biological research with four RF channels and 1H/13C/15N cryogenic and room temperature triple probes with pulsed field gradients
  • 600MHz Bruker Avance III NMR spectrometer with four-channel capability and 1H/13C/15N cryogenic and room temperature triple PFG probes as well as a 1H dedicated probe.



Recently installed Bruker Avance III spectrometer with liquids and solids capabilities.

Leadership and Contact


 

Leonard Spicer, PhD

Director
919.684.4327
spicer@biochem.duke.edu

Leonard Spicer, PhD

spicer@biochem.duke.edu
919.684.4327

Email Me!

Ronald Venters, PhD

Associate Director
919.613.8888
venters@duke.edu

Ronald Venters, PhD

venters@duke.edu
919.613.8888

Email Me!

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Locations

  • Rooms B 138-147, Levine Science Research Center, Durham, NC 27710 (Main Facility)
  • Rooms 1240-1241, French Family Science Building , Durham, NC 27710 (Satellite Facility)
Click Here To Visit The High Resolution NMR Spectroscopy Website

High-Throughput Screening*


The High-Throughput Screening (HTS) Shared Resource (a developing CCSG shared resource) provides expertise, infrastructure and reagents for high-throughput screening of chemical, RNAi, CRISPR and open reading frame (ORF) libraries. The multiple screening platforms supported by the facility enable systematic, comprehensive interrogation of gene function, cellular phenotypes or molecular interactions that provide opportunities for unbiased discovery of novel biology. The facility also provides reagents and advice for low-throughput functional experiments, including individual CRISPR, ORF and shRNA vectors.

So Young Kim, Ph.D.

Director

So Young Kim, Ph.D.

soyoung.kim@duke.edu

Email Me!

The rapidly developing functional genomic technologies available today provide unprecedented opportunities for gaining insight into gene function and discovering novel drug targets or lead compounds for clinical applications.



The rapidly developing functional genomic technologies available today provide unprecedented opportunities for gaining insight into gene function and discovering novel drug targets or lead compounds for clinical applications.

So Young Kim, Ph.D.

Director

So Young Kim, Ph.D.

soyoung.kim@duke.edu

Email Me!

Services


  • Compound screening
  • The shared resource performs compound screens in 96- or 384-well microplate format using screener-provided or facility in-house libraries, which range in size from 100-50,000 compounds.
  • Loss-of-function screening (CRISPR and RNAi)
  • The shared resource maintains siRNA (Qiagen Human Genome siRNA library) and lentiviral shRNA (Sigma Mission) libraries for screening. Individual shRNA clones from the Mission library are also available to investigators. Lentiviral CRISPR sgRNA mouse and human genome libraries are available for pooled screening.
  • Gain of function screening
  • The shared resource offers gain-of-function screening through overexpression of open reading frames (CCSB-Broad Lentiviral ORF Expression Kinase Collection) to characterize the effects of kinase overexpression in various contexts.
  • Custom CRISPR vector production
  • The shared resource offers custom CRISPR sgRNA vector construction services, which include design, vector cloning and experimental validation. Vectors for transient expression and viral transduction are available.
  • Phenotypic/Molecular quantitative assays
  • The shared resource has a Cellomics ArrayScan high-content screening system for automated image acquisition and analysis in multiwell plates. There are also two multimodal plate readers for sensitive detection of absorbance, fluorescence intensity, fluorescence polarization, FRET, time-resolved fluorescence, BRET and luminescence. The Clariostar is also capable of kinetic assays, spectral scans and has dual injectors.

Equipment


  • Labcyte Echo acoustic dispenser
  • Velocity11 system with Bravo liquid handler, integrated with plate labeler, sealer and stackers
  • Cellomics ArrayScan high-content screening system
  • BMG Clariostar multimodal plate reader
  • Biotek Synergy H1MF multimodal plate reader
  • Additional high-throughput infrastructure, including plate washers and dispensers

Leadership and Contact


 

So Young Kim, Ph.D.

Director
soyoung.kim@duke.edu

So Young Kim, Ph.D.

soyoung.kim@duke.edu

Email Me!

Sandeep Dave, MD

Co-Director
sandeep.dave@duke.edu

Sandeep Dave, MD

sandeep.dave@duke.edu

Email Me!

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Location

  • 0050 CARL Building, 213 Research Drive, Durham, NC 27710
Click Here To Visit The High-Throughput Screening Website

Information Systems


The Duke Cancer Institute Information Systems group (DCI IS) provides information systems to DCI members in support of clinical, translational, and basic biomedical research. The goal of this shared resource is to provide comprehensive computational support to enable researchers to use technology in the most efficient manner possible to accomplish their research goals. It is closely integrated with DCI’s Bioinformatics and Biostatistics Shared Resources. DCI IS is organized into three teams: the service desk/systems team, the application development team including web services, and the database management team. Staff experience includes strong proficiency in clinical trial building and management, website design and administration, application and database development, and information technology infrastructure. Resource personnel provide systems management, network administration, database development/administration, and web/application development/support, plus server and desktop support for over 90 servers and for approximately 1000 users in DCI member laboratories. DCI IS also provides support for large scale servers and software for the DCI’s Biostatistics and Bioinformatics Shared Resources.

Tim Steele, MBA

Manager

Tim Steele, MBA

tim.steele@duke.edu
919.681.5429

Email Me!

Our mission is to provide comprehensive computational support to enable researchers to use technology in the most efficient manner possible to accomplish their research goals. Most DCI members are not experts in information technology and thus require some level of staff support to ensure optimal use of the shared resource.



Our mission is to provide comprehensive computational support to enable researchers to use technology in the most efficient manner possible to accomplish their research goals. Most DCI members are not experts in information technology and thus require some level of staff support to ensure optimal use of the shared resource.

Tim Steele, MBA

Manager

Tim Steele, MBA

tim.steele@duke.edu
919.681.5429

Email Me!

Services


  • Infrastructure, hardware and software to meet the computing needs of DCI members and DCI-based Shared Resources.
  • Expertise in IS options to meet computational needs.
  • Liaison to institution-wide information technology efforts to ensure DCI needs are accounted for.
  • 21CFR Part 11 Compliant Electronic Data Capture (EDC) platform.
  • DCI Reporting Portal, a tool that presents a unified view of clinical research data aggregated across the oncology clinical research unit.

Equipment and Technology


  • Secure data center with a temperature and humidity control with FM200 fire suppression, UPS and emergency generator power protection
  • All servers and workstations are also protected by up to date anti-spyware and anti-virus software
  • Platforms include: Microsoft Windows Server, Red Hat Enterprise Linux, and Debien Linux
  • Supported applications include, SAS, R/Bioconductor, Microsoft SQL Server, Microsoft Office, Oracle databases, Oracle Clinical and Medidata Rave
  • Bio banking informatics for the brain tumor bio repository and the brain tumor immunotherapy program
  • A prediction tool (mCRPC Nomogram) for Metastatic Castrate Resistant Prostate Cancer Patients (MCRPC) used for predicting the overall survival of prostate cancer.

Leadership and Contact


 

Tim Steele, MBA

Manager
919.681.5429
tim.steele@duke.edu

Tim Steele, MBA

tim.steele@duke.edu
919.681.5429

Email Me!

Rollover or click cards for contact information

 

Location

  • 2424 Erwin Road, Suite 702, 11074 Hock Plaza, Durham, NC 27705
Click Here To Visit The Information Systems Website

Light Microscopy


The Light Microscopy Core Facility (LMCF) at Duke serves as the Light Microscopy Shared Resource for the Duke Cancer Institute (DCI). The LMCF provides access to a range of modern imaging systems – confocals (eight), live cell fluorescence microscopes, spinning disk, multiphoton, TIRF and more to allow imaging of samples ranging from fixed immunofluorescence slides and live cell tissue culture models, to model organisms and intravital imaging of mice. Facilities for the accurate processing and analysis of image data are also provided. Training is provided for all aspects of use and the facility is staffed by three full-time PhD research scientists. Educational classes are provided for the theory of microscopy and image processing. Trained users can access the equipment 24 hours a day.

Sam Johnson, PhD

Director

Sam Johnson, PhD

sam.johnson@duke.edu

Email Me!

Microscopy is an essential technique in a wide variety of basic research, but the costly machines needed to perform this research are generally beyond the budgets of most labs. We are here to help people however we can, from showing them how to use the equipment, advising on how to design an experiment, which reagents and methods to use, troubleshooting, to the quantitative analysis and visualization of the images.



Microscopy is an essential technique in a wide variety of basic research, but the costly machines needed to perform this research are generally beyond the budgets of most labs. We are here to help people however we can, from showing them how to use the equipment, advising on how to design an experiment, which reagents and methods to use, troubleshooting, to the quantitative analysis and visualization of the images.

Sam Johnson, PhD

Director

Sam Johnson, PhD

sam.johnson@duke.edu

Email Me!

Services


  • Affordable access to core microscopy technologies including confocal, live cell, spinning disk, multiphoton, and TIRF imaging
  • Image processing and quantification
  • Training and support with all instrumentation and techniques
  • Microscopy and image analysis classes

Equipment


  • 8 Point-scanning confocals – Zeiss 780s, 710, 510s, Leica SP8 and SP5s
  • 3 fluorescence microscopes – Zeiss and Leica upright and inverted
  • Multi-photon – Olympus FV1000
  • Spinning disk – Andor XD revolution
  • DeltaVision deconvolution
  • Live cell stations – Zeiss incubated inverted systems
  • Vivaview incubator microscope
  • TIRF – Leica AM TIRF MC
  • Stereoscope – Lumar V12
  • Laser Capture Microdissection – Zeiss UV-laser based
  • 6 Analysis workstations – software includes Imaris and Volocity 3D visualization and analysis, Huygens and DeltaVision deconvolution, metamorph and FIJI



I-Chien Liao and Kam Leong
Skeletal C2C12 myoblasts differentiated to form myotubes. Actinin Actin DAPI


O’neil Guthrie and Daniel Kiehart
Digestive system of a wandering third instar larva. F-actin lamin DNA

Leadership and Contact


 

Sam Johnson, PhD

Director
Sam.johnson@duke.edu

Sam Johnson, PhD

sam.johnson@duke.edu

Email Me!

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Locations

  • FFSC location: 4215 French Family Science Center, 124 Science Drive, Durham, NC 27710
  • LSRC Location: C167 Levine Science Research Center, 308 Research Drive , Durham, NC 27710
  • Nanaline Duke Location: 337 Nanaline Duke, 307 Research Drive, Durham, NC 27710
  • Research Park 2 Location: 111 Research Park II, 10 Circuit Drive, Durham, NC 27710
Click Here To Visit The Light Microscopy Website

Optical Molecular Imaging and Analysis


The Optical Molecular Imaging and Analysis (OMIA) Shared Resource provides a variety of optical imaging services, technologies, equipment and expertise to support the scientific needs and objectives of the Duke Cancer Institute (DCI). Optical techniques have become an important tool for understanding molecular mechanisms of cancer development and therapy. Its high sensitivity and specificity enable elegant studies into gene regulation and functional processes involved in cancer progression and therapeutic response. Optical techniques are non-invasive and can be done serially in the same animal, allowing for better characterization of transient or dynamic effects and minimizing the overall use of animals.

Gabi Hanna, MD

Associate Director

Gabi Hanna, MD

gabi.hanna@duke.edu
919.684.4890

Email Me!

My philosophy is ‘seeing is believing,’ and we’re trying to take that philosophy as far as possible. With optical molecular imaging, you can look at live single cells in a microscope, or you can study a tumor, or look at the liver, pancreas or other organs.



My philosophy is ‘seeing is believing,’ and we’re trying to take that philosophy as far as possible. With optical molecular imaging, you can look at live single cells in a microscope, or you can study a tumor, or look at the liver, pancreas or other organs.

Gabi Hanna, MD

Associate Director

Gabi Hanna, MD

gabi.hanna@duke.edu
919.684.4890

Email Me!

Services


  • The Optical Molecular Imaging and Analysis shared resource facilitates small animal imaging and spectroscopy. Services can be broken down broadly according to the categories below:
  • Optical imaging using fluorescence and bioluminescence
  • Optical spectroscopy and hyperspectral imaging for functional characterization of tissue oxygenation and other parameters.
  • Window chamber surgery training and support.
  • User training in techniques.
  • Scientific guidance on experimental design, data analysis and interpretation.

Equipment and Technology


  • Microsurgery Suite
  • IVIS Lumina and Kinetic (whole animal fluorescence, bioluminescence, and x-ray imaging)
  • PerkinElmer FMT2500LX fluorescence molecular tomography instrument
  • Intravital microscopy





Left to right: Mark Dewhirst, DVM, PhD, Gabi Hanna, MD, Greg Palmer, PhD

Leadership and Contact


Mark Dewhirst, DVM, PhD

Co-Director
919.684.4180
dewhirst@radonc.duke.edu

Mark Dewhirst, DVM, PhD

dewhirst@radonc.duke.edu
919.684.4180

Email Me!

Greg Palmer, PhD

Co-Director
919.613.5053
greg.palmer@duke.edu

Greg Palmer, PhD

greg.palmer@duke.edu
919.613.5053

Email Me!

Rollover or click cards for contact information

Gabi Hanna, MD

Associate Director
919.684.4890
gabi.hanna@duke.edu

Gabi Hanna, MD

gabi.hanna@duke.edu
919.684.4890

Email Me!

Locations

  • Medical Sciences Research Building (MSRB), Rooms 239, 283, 295, and 296, Durham, NC 27710
  • Genome Sciences Research Building (GSRB) II, Room 1011, Durham, NC 27710
  • Cancer Center Isolation Facility (CCIF), Room 103XR, Durham, NC 27710
Click Here To Visit The Optical Molecular Imaging and Analysis Website

Pharmacokinetics and Investigational Chemotherapy


The Pharmacokinetics and Investigational Chemotherapy Shared Resource provides a broad spectrum of pharmacological and pharmaceutical services essential to conduct preclinical and clinical research in cancer biology, drug discovery, drug evaluation, and related areas by members of the Duke Cancer Institute (DCI) and other Duke researchers. It is composed of two services: the Pharmacokinetics service and the Investigational Chemotherapy Service (ICS).

         The pharmacokinetics/pharmacodynamics (PK/PD) and small molecule analytical services (drugs, drug metabolites, physiological metabolites, biomarkers, etc.) are provided by the PK/PD Core which is located in a custom-designed analytical laboratory area in South Hospital and is contiguous with the new Duke Cancer Center building. It is managed by DCI and is equipped with state-of-the-art analytical (HPLC,LC/MS/MS) and computational (WinNonlin, SAAM II) equipment and staffed with skilled and knowledgeable personnel. Comprehensive PK support includes: study design, IACUC protocol, drug administration, bioanalytical assay development/validation, PK analysis, reports, publication, and grant application. The mission of the resource is to provide expert, timely, and cost-effective analytical and PK/PD support for Duke researchers and outside collaborators involved in basic, preclinical, and clinical studies.

        The ICS is a part of the Department of Pharmacy and is located within the Cancer Center Infusion Pharmacy. The ICS prepares and dispenses investigational drug products, maintains drug accountability records and investigational drug inventories according to FDA and CTEP guidelines, and provides design consultation, professional staff education, and implementation services for clinical research studies. The ICS is managed by a clinical pharmacist in the Department of Pharmacy, and is staffed by a clinical pharmacist, a clinical research coordinator and a clinical research specialist.

Beth McLendon-Arvik, PharmD

Manager, Investigational Drug Services (ICS/IDS)

Beth McLendon-Arvik, PharmD

beth.mclendon@duke.edu
919.681.2752

Email Me!

The clinical pharmacy services we offer help to provide safety and maintain the integrity of research studies at the DCI. We prepare investigational drug products, maintain drug accountability records and investigational drug inventories according to guidelines, and also provide design consultation, professional staff education, and implementation services for clinical research studies.



The clinical pharmacy services we offer help to provide safety and maintain the integrity of research studies at the DCI. We prepare investigational drug products, maintain drug accountability records and investigational drug inventories according to guidelines, and also provide design consultation, professional staff education, and implementation services for clinical research studies.

Beth McLendon-Arvik, PharmD

Manager, Investigational Drug Services (ICS/IDS)

Beth McLendon-Arvik, PharmD

Beth.mclendon@duke.edu
919.681.2752

Email Me!

Services


  • Services provided by the PK/PD Service:
  • Assay development and validation
  • Targeted Quantitative Analysis
  • Drugs
  • Drug metabolites
  • Physiological metabolites
  • Cancer biomarkers
  • Oxidative-stress biomarkers
  • Any other small molecule of interest in:
  • Bodily fluids: plasma, serum, blood, urine, milk, synovial fluid, lymph aspirate, etc.
  • Tissues: vital organs (liver, kidney, brain, etc), tumor, bone, skin, hair
  • Cell culture: cell pellets, cell lysates, media
  • Comprehensive PK/PD Service
  • In-vitro drug stability and metabolism (ADME)
  • Drug metabolite identification
  • Drug formulation and route of administration optimization
  • Species selection for optimal preclinical studies (mouse, rat, rabbit, dog, pig, non-human primates)
  • Preclinical PK/PD experiment (animal DLAR protocol, drug administration, sample collection/storage)
  • Drug/metabolite assay development (LC-MS/MS, HPLC, ELISA)
  • Compartmental/non-compartmental modelling (WinNonlin, SAAM II + PopKinetics)
  • Assistance in data interpretation, reporting/publishing, and funding application
  • Services provided by the Investigational Chemotherapy Service:
  • Major Services
  • Investigational drug product preparations and maintaining drug accountability records and investigational drug inventories
  • Consultation regarding research study design
  • Implementation of new research studies and conducting professional staff education regarding investigational drug studies
  • Pharmacy review of protocols for Cancer Protocol Review Committee and Institutional Review Board
  • Protocol Specific Services include
  • Preparing online pharmacy procedures/drug data sheet
  • Creating the medication orderable build in Epic EHR and collaborating with study team to create the study protocol template. Randomization, secure storage, accountability, blinding, preparation/compounding, patient counseling, staff education, records management
  • Audits (CDQA, Sponsor), Inspections (FDA)
  • Ensure adherence to USP standards

Equipment


  • The Investigational Chemotherapy Service’s major equipment includes:
  • Investigation drug research software – Vestigo
  • Six refrigerators (4 degree C)
  • Two freezers (-20 degrees C)
  • Two ultra-low freezers (-80 degrees C)
  • Fume hood for oral study preparation
  • Dedicated clean room for gene therapy/viral vector preparations
  • Investigational Chemotherapy Pharmacy Facility (room 4N33) co-located with the Cancer Center Infusion Pharmacy (room 4N31)
  • The PK/PD Core’s major equipment includes:
  • Applied Biosystems/SCIEX API 5500 QTrap + Agilent 1200 series LC
  • Applied Biosystems/SCIEX API 4000 QTrap + Shimadzu 20A series LC
  • Waters 2695 conventional HPLC
  • Waters 2475 scanning fluorescence detector
  • Waters 2487 dual wavelength uv/vis detector
  • SPECTRAmax 250 (Molecular Devices) plate reader with SoftMAX Pro software
  • Win Nonlin and SAAM II v2.3 + PopKinetics software
  • Lab DATA system managed by DCI-IS (weekly backup)
  • Two refrigerators (4° C)
  • Two low temp. freezers (-20° C)
  • Three ultra-low temp. freezers (-80° C)
  • Two biohazard hoods



Typical Project: Plasma/blood and vital organ pharmacokinetic profiles of a prospective anti-cancer agent.


Rodent PK/PD STATION (stereo-microscope, anesthesia machine, ventilator, hood, etc)


The facility is managed by DCI under the leadership of Ivan Spasojevic, PhD, Co-Director. PK experiments and analysis is performed by Ping Fan, MS, and by students and fellows under supervision.

Leadership and Contact


Paul Bush, PharmD, MBA, FASHP, BCPS

Co-Director
919.681.2755
paul.bush@duke.edu

Paul Bush, PharmD, MBA, FASHP, BCPS

paul.bush@duke.edu
919.681.2755

Email Me!

Beth McLendon-Arvik, PharmD

Manager, Investigational Drug Services (ICS/IDS)
919.681.2752
beth.mclendon@duke.edu

Beth McLendon-Arvik, PharmD

beth.mclendon@duke.edu
919.681.2752

Email Me!

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Ivan Spasojevic, PhD

Co-Director, ICS
Director, PK/PD Core Lab
919.684.8311
ivan.spasojevic@duke.edu

Ivan Spasojevic, PhD

ivan.spasojevic@duke.edu
919.684.8311

Email Me!

Locations

  • Investigational Chemotherapy Service
  • Ambulatory Duke Cancer Center building, Room 4N33
  • Duke Hospital Pharmacy
  • 2301 Erwin Road Duke Children’s Hospital and Health Center, Main Entry Level, Durham, NC 27710
  • Duke North Pavilion (Bone Marrow Transplant) Pharmacy
  • PK/PD Service: Duke Clinics Building (Orange Zone, room 5317), 40 Duke Medicine Cir, Durham, NC 27710
Click Here To Visit The Pharmacokinetics And Investigational Chemotherapy Website

Preclinical Translational Research Unit*


The Duke Preclinical Translational Research Unit functions as a preclinical testing core. We are a Duke School of Medicine Core Facility, and a Duke Cancer Institute Pilot Shared Resource. We offer services for all types of preclinical/translational research including cancer and non-cancer related applications. This provides an option for Duke or external investigators to carry out critical in vivo experiments in a semi-independent laboratory, with input and oversight from experts in statistics, medical devices, pharmacokinetics, physiology, regulation, cancer biology, and animal experimentation, while still having available all of the resources and expertise present at Duke. Our goal is to generate high quality, documented data, focusing on:
• Data integrity
• Sound statistical design
• Clinical relevance
• Commercial viability
• Efficient use of resources

Greg Palmer, PhD.

Chief Director

Greg Palmer, PhD.

greg.palmer@dm.duke.edu
919.613.5053

Email Me!

Our mission is to deliver definitive preclinical efficacy and toxicity data in a fast, efficient manner to accelerate translation and bring innovations to the clinic.



Our mission is to deliver definitive preclinical efficacy and toxicity data in a fast, efficient manner to accelerate translation and bring innovations to the clinic.

Greg Palmer, PhD

Chief Director

Greg Palmer, PhD

greg.palmer@dm.duke.edu
919.613.5053

Email Me!

Services


  • Providing expert guidance on appropriate experimental methods and design, data analysis, controls, and sample size. This will ensure the experiment is run the right way the first time, minimizing waste and needless repetition.
  • Developing SOPs for commonly utilized protocols, such as tumor inoculation, tumor growth delay, TCD50, metastasis assays, and toxicity testing. Standard testing procedures are the expected norm in other disciplines such as engineering, and a rigorous set of SOPs would be beneficial to enable comparisons across different studies, which is not directly possible in most cases presently.
  • Support regulatory compliance with IACUC and coordinate with IRB and FDA regulations for smooth translation to clinical trials.
  • Making data available online as it is collected. Every PI/ collaborator will have a secure online account to monitor the progress of work, view reports, raw data and analysis.
  • Providing experienced technicians to carry out the research, document the methodology, and establish traceability of results.

Equipment


  • LABCAT preclinical data management software (www.labcat.com) is used in this core. This is GLP compliant software that facilitates secure electronic medical record keeping for preclinical studies. Features include data collection, study management, data analysis and reporting system for pre-clinical investigations. Original study data is managed through this software which maintains data security and provenance from study design and setup, through data collection and analysis.

Leadership and Contact


Greg Palmer, PhD

Director
919.613.5053
greg.palmer@dm.duke.edu

Greg Palmer, PhD

greg.palmer@dm.duke.edu
919.613.5053

Email Me!

Gabi Hanna, MD

Executive Director
919.667.8571
gabi.hanna@dm.duke.edu

Gabi Hanna, MD

gabi.hanna@dm.duke.edu
919.667.8571

Email Me!

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Mark Dewhirst, DVM, PhD

Senior Advisor
919.684.4180
mark.dewhirst@dm.duke.edu

Mark Dewhirst, DVM, PhD

mark.dewhirst@dm.duke.edu
919.684.4180

Email Me!

Primary Tumor Cell Culture*


Primary Tumor Cell Culture (PTCC), was created with the goal of generating hundreds of primary malignant and normal epithelial cell lines to enable new types of investigations by DCI members. Most commonly used, commercially available cancer cell lines are believed to possess limited genetic or functional heterogeneity relative to the corresponding human disease while also commonly harboring de novo features emerging from long-term selection in in vitro culture conditions. Further, many prominent tumor subtypes are poorly compatible with classical derivation conditions, leading to their poor representation in available cell lines. Recently, the “conditional reprogramming” technique developed by Schlegel and colleagues at Georgetown University (Am. J. Path. 2012, 180: 599) was shown to enable the efficient generation of cell lines from malignant and normal epithelial tissues. This method works by introducing primary tumor cells into specialized culture conditions that include irradiated fibroblast feeder cells and culture media containing a Rho kinase (ROCK) inhibitor. A large fraction of primary epithelial tissue samples, and individual cells within those samples, are observed to proliferate indefinitely under these conditions while maintaining the key genomic features and drug sensitivities of the parental tissues. As such, cell lines derived using conditional reprogramming may be particularly useful for researchers interested in primary cell line models of human cancer, achieving broader representation of the genetic and histological diversity inherent in human tumors, studying drug resistance or intra-/inter-tumor heterogeneity, and studying reference normal human epithelial cells. Together with the Biospecimen Repository and Processing Core and DCI-supported patient-derived xenograft resource, the PTCC will provide a set of powerful and unique tools for DCI members and others.

Kris Wood, PhD

Director

Kris Wood, PhD

kris.wood@duke.edu
919.613.8634

Email Me!

The PTCC is being created to leverage Duke Medicine’s access to large numbers of primary patient-derived tumors to create cell line disease models that will enable a wide range of new investigations by cancer researchers on campus.



The PTCC is being created to leverage Duke Medicine’s access to large numbers of primary patient-derived tumors to create cell line disease models that will enable a wide range of new investigations by cancer researchers on campus.

Kris Wood, PhD

Director

Kris Wood, PhD

kris.wood@duke.edu
919.613.8634

Email Me!

Services


  • Providing primary, early passage, malignant and normal epithelial cell lines from lung, breast, prostate, pancreas, colorectal, cervical/ovarian, bladder/renal or other epithelial cancer types.
  • Generating primary malignant and normal epithelial cell lines for special needs by researchers at DCI and other Duke Units
  • Providing consultation regarding methods for culturing and experimenting with primary cell lines
  • Providing feeder cells and conditioned media

Equipment


  • This shared resource is equipped with standard cell culture and storage equipment like biosafety cabinets, CO2 incubators, a light microscope, a Coulter cell counter/analyzer, refrigerators, liquid nitrogen cryopreservation tanks, a centrifuge, freezers ((-20°C and -80°C) and other common cell culture equipment.

Leadership and Contact


 

Kris Wood, PhD

Director
919.613.8634
kris.wood@duke.edu

Kris Wood, PhD

kris.wood@duke.edu
919.613.8634

Email Me!

Thomas Ribar

Co-Director
919.684.2634
thomas.ribar@dm.duke.edu

Thomas Ribar

thomas.ribar@dm.duke.edu
919.684.2634

Email Me!

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Location

  • CARL Building, Rooms 214, 215, and 218, Durham, NC 27710
Click Here To Visit The Primary Tumor Cell Culture Website

Proteomics and Metabolomics


The Proteomics and Metabolomics Shared Resource provides qualitative/quantitative protein and metabolite analyses, using ultra-performance liquid chromatography and tandem mass spectrometry (UPLC/MS/MS) as its primary tool. Originally designed to provide all needed capabilities for mass spectrometry based proteomics for identification and quantitation, including biomarker discovery and biomarker verification experiments, the resource’s services have been expanded to include qualitative and quantitative metabolite characterization. For ‘omic-scale qualitative and quantitative analyses, the laboratory is equipped with four high-resolution accurate-mass tandem mass spectrometers (MS/MS), each coupled to a dedicated UPLC or UPLC/UPLC system (three hybrid quadrupole time-of-flight systems, and a hybrid quadrupole-orbitrap system. For targeted analyses, including biomarker verification, analyses are performed using UPLC/triple quadrupole tandem mass spectrometer under Multiple Reaction Monitoring conditions (two systems). The laboratory has the tools needed for enrichments (chemical and/or antibody-based) of sub-proteomes based on Post-Translational Modifications, including phosphorylation, acetylation, ubiquitination, methylation, acylation, and S-nitrosylation. The lab also supports structural proteomic studies using Hydrogen-Deuterium Exchange UPLC/MS/MS. Data processing is accomplished using dedicated servers and a dedicated data storage system (two 35 TB mirrors). Protein identifications from MS/MS spectra are accomplished using either of two search engines – Mascot (Matrix Sciences) or IdentityE – (Waters). The Skyline program (MacCoss Lab, U Wash., NCI-CPTAC funded) is used for processing targeted proteomics experiments. Unbiased proteomics quantitation is accomplished using Rosetta Elucidator software, and Progenesis QI is used for untargeted metabolomics. Proteome Software Scaffold software is used for data visualization and for data return to Resource collaborators. The secure web-based “GCB Express” data repository is used for processed data storage/distribution from projects. Data integrity features include data “fingerprinting” on upload, and strict access controls managed by data owners.

Arthur Moseley, PhD

Director

Arthur Moseley, PhD

arthur.moseley@duke.edu
919.684.4456

Email Me!

While very significant insights into biology are contained in gene sequencing and gene expression studies, research projects are more completely informed if they also have qualitative and quantitative data on the ultimate products of gene expression – proteins and metabolites.



While very significant insights into biology are contained in gene sequencing and gene expression studies, research projects are more completely informed if they also have qualitative and quantitative data on the ultimate products of gene expression – proteins and metabolites.

Arthur Moseley, PhD

Director

Arthur Moseley, PhD

arthur.moseley@duke.edu
919.684.4456

Email Me!

Services


  • Unbiased (‘omic) qualitative and quantitative analyses of proteins or metabolites from cells, tissues or biofluids using nanoscale ultraperformance liquid chromatographs (single or multidimensional) coupled to high-resolution accurate-mass tandem mass spectrometers (LC/LC/MS/MS)
  • Targeted qualitative and quantitative analyses of proteins and metabolites via Multiple Reaction Monitoring analyses using stable isotope-labeled standards (ultraperformance liquid chromatographs coupled to triple quadrupole mass spectrometry)
  • Qualitative and quantitative analysis of sub-proteomes based on Post-Translational Modifications including phosphorylation, acetylation, ubiquitination, methylation, acylation, and S-nitrosylation
  • Qualitative and quantitative metabolomics analyses using 7 assays, including targeted and open (‘omic) panels covering polar metabolites and lipids
  • On-site consultation with four PhD-level scientists; full time staff of eight scientists with >90 years of experience in mass spectrometry

Equipment and Technology


  • High resolution accurate mass tandem mass spectrometers for -omic analyses (four systems)
  • Triple Quadrupole tandem mass spectrometer for targeted analyses (two systems)
  • Ultraperformance liquid chromatographs
  • nanoACQUITY (Waters), three systems
  • nanoACQUITY with 2D Technology (Waters), two systems
  • Acquity M-Class (Waters)
  • Conventional Acquity UPLC (Waters), two systems
  • Microfluidics-based nanoscale capillary liquid chromatography (ionKey, Waters)
  • Hydrogen-Deuterium Exchange System (HDX, Waters) for structural proteomics
  • Dedicated high-performance computational resources
  • Two dedicated servers (virtual servers in Duke OIT cluster)
  • Two custom-built 448-core GPU-based workstation ‘supercomputers’
  • Four high-performance PC workstations
  • Two 35 TB data mirrors
  • Dedicated software
  • Elucidator (Rosetta) with Oracle DB
  • Mascot Daemon, Mascot Distiller and Mascot Server (Matrix Sciences)
  • Scaffold and Scaffold Q+S (Proteome Software)
  • ProteinLynx Global Server (Waters)
  • Progenesis QI (Waters)
  • Skyline (MacCoss lab, open-source software created under NCI CPTAC)



G2Si High-Resolution Accurate-Mass Tandem Mass Spectrometer


Mass Spectrometry Image Analysis – mouse brains

Leadership and Contact


 

Arthur Moseley, PhD

Director
919.684.4456
arthur.moseley@duke.edu

Arthur Moseley, PhD

arthur.moseley@duke.edu
919.684.4456

Email Me!

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Locations

  • B02 Levine Sciences Research Center 450 Research Drive, Durham, NC 27710
Click Here To Visit The Proteomics and Metabolomics Website

Sequencing and Genomic Technologies


The Sequencing and Genomic Technologies Shared Resource brings all of the robust genomic technologies on campus under a single organization and enables comprehensive consultation, seamless management of complex projects that span multiple services, enhanced operational flexibility, and economies of scale for support services. Assistance is also provided to investigators with regard to data quality control, versioning, statistical analysis, and dissemination for all of these services. A major goal of many cancer genome projects is to characterize key genetic alterations in cancer and discover therapeutic targets through comprehensive genomic profiling of the cancer genome. The Sequencing and Genomic Technologies Shared Resource provides researchers with comprehensive genomic solutions with the latest and most complementary technologies readily available.

Gregory Wray, PhD

Director of Center for Genomic and Computation Biology

Gregory Wray, PhD

Director of Center for Genomic and Computation Biology

Email Me!

By bringing everything under one roof, we can provide better service and make it much simpler for researchers to find the most appropriate application for their needs. We encourage potential users to schedule a consultation to discuss their experimental design and analysis approaches in advance of securing our services. We can help ensure that investigators consider the entire arc of their project.



By bringing everything under one roof, we can provide better service and make it much simpler for researchers to find the most appropriate application for their needs. We encourage potential users to schedule a consultation to discuss their experimental design and analysis approaches in advance of securing our services. We can help ensure that investigators consider the entire arc of their project.

Gregory Wray, PhD

Director of Center for Genomic and Computation Biology

Gregory Wray, PhD

Director of Center for Genomic and Computation Biology

Email Holly Dressman

Services


  • RNA/DNA extraction, QC, Covaris Shearing
  • Gene Expression Analysis (RNAseq, Targeted RNAseq, microarrays, RTPCR, ddPCR)
  • Sequence Analysis (Functional, Variant Detection, De Novo
  • Single cell isolation and profiling
  • Microbiome profiling

Equipment


  • Three Illumina high-throughput DNA sequencers (HiSeq4000, HiSeq2500, HiSeq 2000, and MiSeq)
  • Pacific Biosciences RSII third-generation DNA sequencer with SMRT technology
  • Two LifeTechnologies IonTorrent high-throughput DNA sequencers (PGM and Proton)
  • Fluidigm C1 Single-Cell Auto-prep and IFC HX and MX controller system
  • Affymetrix GeneChip workstation with four GeneChip Fluidic 450 stations, two Affymetrix hybridization systems, and one Affymetrix GeneChip 7G scanner
  • One Agilent C and two Axon GenePix 4000B scanners
  • Life Technologies ABI 7900HT RT-PCR machine with autoloader, one Applied Bio RT-PCR Machine (steponeplus), Fluidigm BioMark HD RT-PCR
  • Bio-Rad QX200 Droplet Digital PCR System

Leadership and Contact


Gregory Wray, PhD

Director of Center for Genomic and Computation Biology
919.684.6696
gwray@duke.edu

Gregory Wray, PhD

gwray@duke.edu
919.684.6696

Email Me!

Holly Dressman, PhD

Co-Director
919.668.1583
holly.dressman@duke.edu

Holly Dressman, PhD

holly.dressman@duke.edu
919.668.1583

Email Me!

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Olivier Fedrigo, PhD

Co-Director
919.684.6730
ofedrigo@duke.edu

Olivier Fedrigo, PhD

ofedrigo@duke.edu
919.684.6730

Email Me!

Locations

  • Biological Sciences Building, Rooms 119, Durham, NC 27710

SERVICES: DNA sequencing, RNA sequencing, Chromatin Immunoprecipitation Sequencing, DNA Modification Sequencing

Email: sequencing@duke.edu
  • 2208B CIEMAS, Durham, NC

SERVICES: Microarray – Agilent and Affymetrix, Single cell isolation and profiling, Microbiome profiling, Sample Processing & QC – Covaris Shearing, Sample Processing & QC – DNA/RNA extraction, Sample Processing & QC – DNA/ RNA QC, Sample Processing & QC – Beta Globin Reduction, RT-PCR – ABI 7900 HT and Fluidigm RT-PCR, droplet digital PCR-Biorad QX200, Instrument & Software Usage

Email: microarraylab@duke.edu
Click Here To Visit The Sequencing and Genomic Technologies Website

Transgenic and Knockout Mouse


The Transgenic and Knockout Mouse Shared Resource provides DCI members comprehensive and user friendly services for the production of custom designed, genetically altered, transgenic and gene targeted mice, as well as the ability to cryopreserve these valuable reagents for storage & distribution to the scientific community. The resource is organized into three teams of specialized personnel who provide the following services: 1) molecular biology service (including targeting constructs and CRISPR reagents), 2) transgenic and gene targeted mouse service, and 3) rodent husbandry service. Each team of experts functions as working partners with basic and clinician scientists at the bench. These teams can also provide personalized technical support at all stages of the production process, including new approaches to conditional mutagenesis, breeding, and the use of related mutant mice or cells that are already available from other resources located worldwide. The following services are offered by this resource: construction & design of embryonic stem cell (ESC) targeting vectors by BAC Recombineering, with primers for screening & control vector; ESC targeting, selection, PCR Screening with expanding & freezing multiple clones; validation of targeted clones by SA & LA PCR & Southern blotting; injection of validated ESC clones to create chimeric mice; breeding & expansion of chimeric mouse lines; CRISPR-mediated genome editing in mouse embryos, cryopreservation of mouse embryos & sperm; DNA microinjection to produce transgenic mice; CRISPR construct microinjection into 1 cell embryos and related activities.

Scott Soderling, PhD

Director

Scott Soderling, PhD

scott.soderling@dm.duke.edu
919.684.9001

Email Me!

The Transgenic Core supports DCI investigators by providing a full range of options for generating custom mice genetically altered for their cancer research. Users can literally name their gene of interest and the type of alteration they desire and received their mice. For projects handled by the core from start to finish to generate approximately a 98 percent success rate.



The Transgenic Core supports DCI investigators by providing a full range of options for generating custom mice genetically altered for their cancer research. Users can literally name their gene of interest and the type of alteration they desire and received their mice. For projects handled by the core from start to finish to generate approximately a 98 percent success rate.

Scott Soderling, PhD

Director

Scott Soderling, PhD

scott.soderling@dm.duke.edu
919.684.9001

Email Me!

Services


  • Construction & design of ESC targeting vectors by BAC Recombineering, with primers and control vector for screening recombinants
  • Cloning of CRISPR guide sequences, production of CRISPR sg RNA via in-vitro transcription, CRISPR founder screening and Allelic cloning
  • ESC targeting, selection, PCR screening followed by expanding & freezing multiple clones
  • Validation of targeted clones by PCR & Southern blotting
  • Injection of validated ESC cells to create chimeric mice
  • Breeding chimeras & expansion of mouse lines
  • Cryopreservation of mouse embryos & sperm
  • DNA/RNA (CRISPR) Microinjection to produce transgenic mice

Equipment


  • The resource has equipment associated with rodent housing, including appropriate cages and racks; microinjection set up, needle puller, dissection microscopes, cell culture microscopes, anesthesia device, incubators, PCR machines, centrifuges, and computers.

Leadership and Contact


Scott Soderling, PhD

Director
919.684.9001
scott.soderling@dm.duke.edu

Scott Soderling, PhD

scott.soderling@dm.duke.edu
919.684.9001

Email Me!

John Norton, DVM, PhD

Co-Director
919.684.4204
john.norton@duke.edu

John Norton, DVM, PhD

john.norton@duke.edu
919.684.4204

Email Me!

Rollover or click cards for contact information

Cheryl Bock

Transgenic Facility Manager
919.684.3197
cbock@duke.edu

Cheryl Bock

cbock@duke.edu
919.684.3197

Email Me!

Locations

  • GSRB1, Rooms: Laboratory 3022, Cell Culture 3038, Office 3010, Durham, NC 27705
  • BAC Recombineering Core, Nanaline Duke, Room: 373, 4515 Research Drive, Durham, NC 27710
Click Here To Visit The Transgenic And Knockout Mouse Website