Brian Brunk, Ph.D.
Director
1313 Blockley Hall
215-573-3118
brunkb@pcbi.upenn.edu

The Penn Bioinformatics Core was established in order to provide compute resources, support and training to the University of Pennsylvania biomedical research community. Our goal is to ensure that scientists across the University are able to effectively exploit existing and emerging computational technologies, especially related to genomics scale datasets. To this end we provide consulting and support for experimental design and analysis of microarray experiments and sequence based analyses such as comparative genomics, database queries, motif analyses, promoter analyses etc. We also provide data integration services, database services and scripting to enhance efficiency and productivity of Penn researchers. We have high throughput computing capabilities and provide desktop software to researchers at greatly discounted rates. We provide support to scientists one-on-one and in small groups and also present monthly workshops on various bioinformatics topics.

Biomedical Imaging Core

Cell Center

Tapan Ganguly, Ph.D.
Director
D2 Richards
215-573-7238
gangulyt@mail.med.upenn.edu

The Cell Center Stockroom was established to offer the greatest variety of bioreagents possible while maintaining maximum convenience and savings of time and money to investigators throughout both the Medical Center and the University of Pennsylvania in its entirety.

Cell Center Services, the service component of the Cell Center provides training, and services in various cell culture and associated procedures in addition to preparing specialized cell culture media and molecular biological reagents.

CDB/CVI Microscopy Core

Andrea L. Stout, Ph. D.
Director, Microscopy Core Facility

215-573-3942

astout@mail.med.upenn.edu

The CDB/CVI Microscopy Core is a full-service facility serving the entire University of Pennsylvania community. Our aim is to provide personalized assistance on all aspects of imaging, from tips on sample preparation to training on one of our microscopes to processing and analysis of image data. Our facility currently houses five light microscopes, a scanning electron microscope, and several computers dedicated to image processing and analysis.

DNA Sequencing Facility

Tapan Ganguly, Ph.D
Director
B-1 Richards Basement
(215) 573-7238
dnaseq@mail.med.upenn.edu

The DNA Sequencing Facility provides DNA sequencing, sequence analysis, Genescan (fragment sizing), oglio synthesis and other molecular biological services to the Penn research community and at large. The Facility provides the following services: Automated Cycle Sequencing, Oligonucleotide Synthesis, Large Sequencing Projects, Template Preparation and Purification, GeneScan and Sequence Analysis and Database Searches.

Flow Cytometry and Cell Sorting Facility

Jonni S. Moore, Ph.D.
Director
297 John Morgan Building/6082 (central facility)
762 BRB II/III (satellite facility)
215-898-6853
moorej@mail.med.upenn.edu

Charles "Hank" Pletcher, Jr.
Technical Director
297 John Morgan Building
215-898-3528
pletcher@mail.med.upenn.edu

The Abramson Cancer Center Flow Cytometry and Cell Sorting Facility serves at the University’s core facility and is dedicated to providing all investigators at the University of Pennsylvania access to high quality, cost-effective services as well as the scientific expertise necessary to use this technology in their research effort. It is the largest academic flow cytometry core laboratory in the country and houses 4 cell sorters, 8 tabletop analyzers, and a staff of 5 support investigators.

Penn Microarray Facility

Don A. Baldwin, Ph.D.
Office: 277 John Morgan Bldg.
Instrumentation: 210 John Morgan Bldg.
Sample preparation: 306 Stellar-Chance
215-898-3675
Fax: 898-4227
dbaldwin@mail.med.upenn.edu

The Penn Microarray Facility will provide instrumentation and expertise for RNA transcript profiling. DNA microarrays provide a highly parallel means of measuring the abundance of RNA for targeted genes in a biological sample. The Facility supports two microarray formats: oligonucleotide arrays synthesized by Affymetrix Inc. and arrays of cDNAs printed in-house on glass slides. This reflects our goal of offering a range of cost and performance options suitable for a variety of experimental questions. Researchers from the University and its affiliated institutions are invited to utilize the Microarray Facility as part of their functional genomics efforts, and projects from non-affiliated institutions will be considered by special arrangement. All projects are initiated only after consultation with the facility director; this will ideally occur during the experimental design stage to ensure maximal and meaningful results.

Molecular Diagnosis and Genotyping Facility

Don A. Baldwin, Ph.D.
Director
dbaldwin@mail.med.upenn.edu
Molecular Diagnosis and Genotyping Facility
7 Gates and Maloney Buildings
Hospital of the University of Pennsylvania
Philadelphia, PA 19104-4283
215-662-6589
Fax: 215-614-1986

Kathakali Addya, PhD.
Technical Director
7 Gates and Maloney Buildings
Hospital of the University of Pennsylvania
215-662-7570
addya@mail.med.upenn.edu

The Molecular Diagnosis and Genotyping Facility provides molecular biology assays and single nucleotide polymorphism (SNP) genotyping services to Cancer Center investigators. Molecular assays are critical to many aspects of basic, clinical, and population research, including molecular stratification of patients entering clinical protocols, molecular epidemiologic and pharmacogenetic studies, and longitudinal follow-up of patients in clinical investigations. Since molecular technologies and instrumentation are evolving rapidly, the centralization of molecular testing services within this core facilitates utilization of leading-edge molecular analyses by Cancer Center investigators. Because some assays are used for clinical decisions during clinical trials, tests are meticulously designed and performed with strict attention to the prevention of polymerase chain reaction (PCR) contamination.

Proteomics Core Facility

Chao-Xing Yuan, Ph.D.
Technical Director
853 BRB II/III
215.573.9883
yuancx@mail.med.upenn.edu

The Proteomics Core Facility provides state of the art 2-dimesional differential in-gel electrophoresis and mass spectrometry technologies for the identification of proteins in complex samples. Currently, the core offers the following services:

2D Large Format Gel (26 x 20 cm)
2D Small Format Gel (8 x 10 cm)
SYPRO Ruby Staining and Scanning
Cy2,3,5 Dye labeling and Scanning
Full service image analysis, per hour
Spot picking (robotic), per 96-well plate
Trypsin Digestion
MALDI-TOF peptide mapping
Microflow RP-HPLC/MS/MS
Nanospray high resolution LC/MS/MS
Mass Spectrometry Analysis/Database Search
MALDI-TOF/MS/MS peptide mapping

Research Instrumentation Shop

William Pennie
Acting Manager
75 John Morgan Building/6055
215-898-3663
wpennie@mail.med.upenn.edu

Michael Carman
Instrument Design Specialist
75 John Morgan Building/6089
215-898-3663/5759
mcarman@mail.med.upenn.edu

The Research Instrumentation Shop is a Service Center of the University of Pennsylvania School of Medicine. Its mission is to assist University faculty in the design and construction of both laboratory and clinical instrumentation. The staff is comprised of mechanical, optical, and electronic specialists and is experienced with working with scientists to design and construct custom research instrumentation and apparatus.

Small Animal Imaging Facility

Lewis Chodosh, M.D., Ph.D.
Co-Director
215-898-1321
chodosh@mail.med.upenn.edu

Mitch Schnall, M.D., Ph.D.
Co-Director
215-662-7238
mitchell.schnall@uphs.upenn.edu

Stephen Pickup, Ph.D.
Technical Director
215-349-5257
pickup@mail.med.upenn.edu

The Small Animal Imaging Facility (SAIF) provides multi-modality radiological imaging and image analysis for cells, tissues, and small animals, primarily mice and rats. The assets of the SAIF include state-of-the-art instrumentation and a nationally recognized staff. SAIF currently provides a comprehensive suite of imaging modalities including: magnetic resonance imaging (MRI) and spectroscopy (MRS), optical imaging (including near IR and bioluminescence imaging), computed tomography (CT), positron emission tomography (PET), single photon emission computed tomography (SPECT), and ultrasound (US). In addition, dedicate housing is available for mice and rats undergoing longitudinal imaging studies. Ancillary facilities and resources of the SAIF are devoted to chemistry, radiochemistry, image analysis and animal tumor models.

Transgenic & Chimeric Mouse Facility

Nancy Cooke, M.D.
Director
32 Clinical Research Building
215-898-4425
necooke@mail.med.upenn.edu

Stephen A. Liebhaber, M.D.
Facility Co-Director
215/898-7834
liebhabe@mail.med.upenn.edu

Jean Richa, Ph.D.
Technical Director
215-573-3023
jricha@mail.med.upenn.edu

The Transgenic & Chimeric Mouse Facility provides a centralized service to efficiently produce infection-free transgenic founder and chimeric strains of mice carrying transgenes or gene "knockouts" of specific interest to individual Penn researchers at below cost. The Facility offers services such as DNA injection into fertilized oocytes, ES cell injection into blastocysts, and embryo cryopreservation, along with the care and housing of the mice up to the stage where they would be transferred to the participating investigator.

Vector Core

Julie Johnston, Ph.D.
125 South 31st St., Suite 2000/ 3403
215-573-0633
juliej@mail.med.upenn.edu

The Vector Core facility is an important technological resource for the University of Pennsylvania investigators and external investigators interested in the use of vectors for gene transfer. The primary responsibility of this Core is to develop and produce viral vectors for studies in basic research; such studies provide tools critical to the understanding of gene function and development of therapeutic vectors.

Facilities at the School of Medicine: Other Laboratory/Molecular Services:

Biomedical Informatics

David Fenstermacher, PhD.
Director
1318 Blockley Hall
423 Guardian Drive
215-746-8680
dfenster@mail.med.upenn.edu

The mission of Biomedical Informatics is to centralize bioinformatics, computational biology, clinical informatics and biostatistics expertise in order to enable cancer investigators and high-throughput Shared Resources to integrate, analyze and interpret vast amounts of research and clinical data by developing computational tools that are based on unified data models, standardized user interfaces, structured vocabularies and common metadata elements, and new data visualization methods.

Functional Genomics

Jonathan Schug, Ph.D.
Department of Genetics, IDOM
752A Clinical Research Building
415 Curie Boulevard
(215) 898-0773
(215) 573-2326
jschug@mail.med.upenn.edu

The global aim of the Functional Genomics Core is to provide our clients with a complete microarray and/or high-throughput sequencing package, from the initial steps of experimental design to the final steps of result interpretation and publication.

Penn Gene Targeting Service

Tobias Raabe, Ph.D.
Technical Director
3700 Hamilton Walk
B-1 Richards Bldg
215-898-5762
raabe@mail.med.upenn.edu

The Penn Gene Targeting Service provides a full DNA-to-mouse service that is available to all Penn researchers and all academic researchers outside. Due to increased demand it has recently expanded and has so far produced several conditional and conventional KO mice. The service includes design and construction of targeting vectors (together with the Penn DNA Sequencing Facility), electroporation and selection of vectors into several different mouse ES cell lines and, together with the customer, isolation of ES cell DNA followed by Southern/PCR screening to identify correctly recombined clones. Recombinant clones are tested by the service for cytogenetic integrity and expanded for injection into blastocysts. Timing of the expansion is coordinated with the Transgenic and Chimeric Mouse Facility which performs the injection and produces the chimera. Prices are low compared to comparable commercial facilities. For more information please contact Dr. Tobias Raabe.

Radioimmunoassay Service

Bryan Wolf, M.D., Ph.D.
Director
510 Stemmler Hall
215-898-0025
wolfb@mail.med.upenn.edu

Heather Collins, Ph.D.
Technical Director
510 Stemmler Hall
hwc@mail.med.upenn.edu

This service offers radioimmunoassay and metabolic screening to investigators within the University of Pennsylvania and at surrounding research facilities. The Core assays samples for insulin, glucagon, somatostatin, or C-peptide against standard curves with human, porcine or rat insulin, bovine/procine (mixture) glucagon, mammalian somatostatin-14, and human C-peptide, respectively. Two antisera of differing sensitivity, as well as, microassays are available for the determination of insulin.

Xenograft Core Facility

Gwenn-ael H. Danet-Desnoyers, PhD
710 BRB II/III
215-746-0181
gdanet@mail.med.upenn.edu

The Xenograft Core facility is a research Core that maintains strains of immunocompromised mice for xenograft experiments. Current available strains include NOD/SCID and NOD/SCID/IL2 receptor null (NOG) mice. There are two separate animal colonies to facilitate experiments. The colony in the John Morgan facility has an irradiator available within the animal facility. A new animal colony at the Hill Pavilion has an irradiator and Xenogen Imaging System within the suite. Current established models include xenografting of normal hematopoietic stem cells, AML, ALL, ovarian and lung cancer models. For consultation or question, contact Gwenn Danet.

Facilities at the School of Medicine: Clinical Health Service Research Cores:

Clinical Cell and Vaccine Production Facility

Bruce L. Levine, Ph.D.
Director
BRB II/III
421 Curie Boulevard
215-573-6788
levinebl@mail.med.upenn.edu
www.uphs.upenn.edu/abramson/clinicalFacility.html
www.med.upenn.edu/bmcrc/CCVPF/?CCVPF

The Clinical Cell and Vaccine Production Facility (CVPF) is a core facility within the Abramson Cancer Center of the University of Pennsylvania that can perform processing of a variety of cell types in support of adoptive cell therapy clinical trials. A variety of cell-based therapies involving bone marrow derived cells such as lymphocytes, dendritic and stem cells are currently ongoing or in development. In addition, non-marrow derived cells such as neural stem cells, islet cells and myoblasts can be processed in the CVPF. Processing includes isolation/enrichment of particular cell lineages, cryopreservation and storage of cells and tissues, RNA isolation from tumor, growth and expansion of cells, and transduction (insertion) of experimental therapeutic genes into cells.

Clinical Research Computing Unit (CRCU)

J. Richard Landis, Ph.D.
Core Director
600 Blockley Hall/6021
215-573-4922
jrlandis@cceb.upenn.edu

Harold I. Feldman, M.D., M.S.C.E.
Core Director
Suite 923, Blockley Hall/6021
215-898-0901
hfeldman@cceb.med.upenn.edu

Robert M. Curley, M.S.
Director, Project Operations and Data
Coordination
Suite 560, 3535 Market/3309
215-573-4422
rcurley@cceb.upenn.edu

James L. Kaylor, M.S.E.
Director, Information Services and Technologies
Suite 560, 3535 Market/3309
215-573-4422
jkaylor@cceb.upenn.edu

The CRCU is a designated "Core Research Facility" for the University of Pennsylvania. The unit was formed in 1997 within the Center for Clinical Epidemiology and Biostatistics (CCEB).
Its mission is to provide a suite of collaborative services to support research project development and implementation; and research computing environments within the University. These services include proposal development; project management; operational compliance and regulatory practices; clinical data management; software systems and database design, development, and implementation; and research and academic computing support essential to the conduct of clinical research projects, including multicenter clinical trials, throughout the University of Pennsylvania Health System.

Flow Cytometry and Cell Sorting Facility

Hematopoietic Stem Cell and Leukemia Core Facility

Martin Carroll, M.D.
Associate Director
708 BRB II/III
215 573-5217
carroll2@mail.med.upenn.edu

Czarek Swider
Room 778 BRB II/III
215-898-3974
cswider@mail.med.upenn.edu

This Core facility is focused on facilitation of research involving primary human tissues. We can provide adult bone marrow or fractions of bone marrow to investigators. CD34 cells are available on a routine basis; other cell fractions are available by arrangement. We also maintain a tissue bank of hematopoietic malignancies including AML, ALL, CML, MDS and MPD's. All samples are fully annotated and frozen as viable cells. Expertise on culture and manipulation of primary cells is available. There is also a Miltneyi AutoMacs machine available in the facility for immunomagnetic sorting of large samples for research purposes.

Human Immunology Core

Carl H. June, MD
Director
554 BRB II/III
421 Curie Blvd
215-662-2382
cjune@mail.med.upenn.edu

Jean D. Boyer, Ph.D.
Technical Director Rm. 505 SCL
422 Curie Blvd.
215-662-2382 (Office)
boyerj@mail.med.upenn.edu

The Human Immunology Core will provide expertise and instrumentation for the analysis of immune function in patients during treatment with anticancer drugs and immunotherapy. The Core will serve as a central facility for incorporating the newest technologies and performing validated immunology assays for phase I/II clinical studies, while also offering expert scientific and technical consultations to users interested in conducting this kind of innovative research.

Investigational Drug Service
Kenneth A. Rockwell, Jr., PharmD, MS
Director
IDS, Ground Maloney
(215) 349-8817
ken@spirit.gcrc.upenn.edu

The Investigational Drug Service (IDS) is a research pharmacy charged with the management of research medications used in clinical (human) drug trials, as well as the oversight of medication use in drug trials conducted throughout the University of Pennsylvania and its affiliates. Agents overseen by the IDS include drugs, natural products, vitamins, biologics and gene therapy agents.

Facilities at the School of Medicine: Other Clinical Health Research Services:

Biomedical Informatics

David Fenstermacher, PhD.
Director
1318 Blockley Hall
423 Guardian Drive
215-746-8680
dfenster@mail.med.upenn.edu

The mission of the Biomedical Informatics Core is to centralize bioinformatics, computational biology, clinical informatics and biostatistics expertise in order to enable cancer investigators and high-throughput Shared Resources to integrate, analyze and interpret vast amounts of research and clinical data by developing computational tools that are based on unified data models, standardized user interfaces, structured vocabularies and common metadata elements, and new data visualization methods.

Facilities at the School of Arts and Sciences

Nucleic Acid Facility

Ponzy Lu, Ph.D.
Facility Director
337 Cret Chemistry Building
215/898-1584
ponzy@mail.med.upenn.edu

Xiaolin Zhang, Ph.D.
Technical Director
xzhang@sas.upenn.edu

Regional Laser and Biomedical Technology Laboratories (RLBL)

Prof. Robin M. Hochstrasser
University of Pennsylvania
231S 34th Street
Philadelphia, PA 19104-6323
(215) 898-3605/3610
Fax: (215) 573-2112
ttroxler@mail.sas.upenn.edu

Facilities at the School of Dental Medicine

Biacore Facility Core

Dr. Gary Cohen, Director
216 Levy Building
215-898-5914
cohen@biochem.dental.upenn.edu

Flow Cytometry and Amnis ImageStream Facility

Dr. Bruce Shenker, Director
312 Levy Building
215-898-5959
shenker@pobox.upenn.edu

Laser Confocal Microscope
Dr. Kelly Jordan-Sciutto, Director
312 Levy Building
215-898-4196
jordan@path.dental.upenn.edu

Scanning Electron Microscope (SEM) Core Facility
Dr. Ellis Golub, Director
544 Levy Building
215-898-4629
ellis@biochem.dental.upenn.edu

Tissue Processing Laboratory
Dr. Edward Macarak, Director
426 Levy Building
215-898-8993
macarak@biochem.dental.upenn.edu

Transmission Electron Microscopy Facility
Dr. Edward Macarak, Director
416 Levy Building
215-898-8993
macarak@biochem.dental.upenn.edu

Facilities at the School of Veterinary Medicine

DNA Core Facility

The DNA core facility offers DNA sequencing and for details contact: Dr. Ji-Kang Fang at 215.898.6651.

Flow Cytometry Satellite

The flow cytometry core housing our two units will be located on the third floor of the Hill Pavilion and jointly managed under the School of Medicine Flow Cytometry and Cell Sorting Resource Laboratory (FCCSRL).

Please visit www.med.upenn.edu/bmcrc for information on rates, all locations and training, or call the core lab at 215.898.3528. Training is required before using the facility.

The two SVM units located on the third floor of the Hill Pavilion are:

A BD FACS Canto was recently installed: FACSCanto II Flow Cytometry System is capable of detecting 6 fluorescence colors with dual laser (488nm and 633nm) excitation. The BD FACSCanto II boasts a new fluidic and optical design, which allows for high acquisition speed and low sample carryover. Fully digital electronics make for easier multicolor compensation.

The BD FACSCalibur is a two-laser (488nm and 635nm), four-color analog analyzer.

To further inquire about the services offered, training, and the fee structure by the FCCSRL, contact the Technical Director, Hank Pletcher, at 215.898.3528.

Penn Vet Imaging Facility

Penn Vet's Imaging Facility is located on the third floor of the Hill Pavilion. The core houses a new (4 laser) two-photon/cofocal laser scanning spectral imaging Leica SP5 system on a DM6000 microscope and a (2 laser) Yokagawa CSX-1 spinning disk confocal configured with a Leica DMI4000 microscope. These instruments will provide capability for fixed specimen, in vivo and live cell optical micro-imaging. The Department of Pathobiology will maintain and oversee the fee structure for this service center.

To inquire further about this core facility, please contact the technical director, Dr. Ling-Li Zhang at 215 746-0471or the Department of Pathobiology at 215.746.2046.

Proteomics Core Facility

The School of Veterinary Medicine has a proteomics core facility with a nanobore L/MALDI-Q Star System for characterization of proteins and peptides. Peptides from proteomics or in-gel digested material can be analyzed by MS and sequenced by MS-MS analysis.

The facility also offers specialized services on phospho-peptide mapping and characterization of acetylated proteins. For further information on services and fee schedule contact: Dr. Ji-Kang Fang at 215.898.6651.

Facilities at the Children's Hospital of Philadelphia

BSL3 Cell Sorting Facility

Paul Hallberg, Dedicated Operator
267-426-7177
hallberg@email.chop.edu

Stokes Research Institute

David Pleasure, M.D.
Director
34th & Civic Center Blvd.
215-590-3800
pleasure@email.chop.edu

Facilities at Wistar Institute

Wistar Institute

Giovanni Rovera, M.D.
Director
3601 Spruce Street
215-898-3926
rovera@wista.wistar.upenn.edu

William Wunner
Director
Wistar Biotechnology Resource Facilities
215-898-3854
wunner@wista.wistar.upenn.edu

Biomedical Research | Clinical and Health Services | Computing | Collaborative Research