Bioinformatics Resources at Penn: Bioinformatics - Core Facilities At Penn

The services offered are given below:
Next Generation Sequence Data Analysis (DNA-seq, RNA-seq, Chip-seq, etc.)
Microarray Data Analysis
Data Analysis Application (Web-based/Desktop-based) Development
Database Development (with Web Services)
Large Scale Biomedical Data Management
Bioinformatics Consulting and Training
Grant Support

Contact Information:
Paul Wang, PhD
Director of Bioinformatics Service Core
Institute for Biomedical Informatics, University of Pennsylvania
206 Richards Building, 423 Guardian Drive,
Philadelphia, PA 19104-6021
email: zhipwang@pennmedicine.upenn.edu
voice: 215-573-3117

The goal at the Center for Host-Microbial Interactions is to establish a convenient ‘in-house’ solution for Penn Vet labs to analyze complex data sets that result from systematic studies of gene expression, microbial whole-genome sequencing, and the composition of microbial communities living on animals.

Contact information:
Dr. Dan Beiting, PhD
Research Assistant Professor,
School of Veterinary Medicine
Department of Pathobiology

Rm 314 Hill Pavilion
380 S. University Avenue
Philadelphia, PA 19104
University of Pennsylvania

Phone: 215-898-9247
Email: beiting@upenn.edu

The Clinical Research Computing Unit (CRCU) is an Academic Clinical Research Organization within the Center for Clinical Epidemiology and Biostatistics (CCEB) in the Perelman School of Medicine at the University of Pennsylvania. Since its inception in 1997, the CRCU has been expertly providing the full range of services essential for the conduct of clinical research projects, including Phase I-IV, multi-center, randomized, clinical trials, registry, and cohort studies utilizing state-of-the-art technology and tools to ensure superior data quality.

The CRCU provides expertise in project management, data coordination and research computing tailored to meet your project requirements. The CRCU project teams partner with the BAC in the project design phase to plan accurate and precise data collection modules and to structure project reports for steady oversight. We specialize in study design and development, site management and training, data collection, processing, quality control, regulatory requirements and reporting, database development, administration, security, data storage and proposal development.

The services offered are given below:
Project Operations & Compliance
Clinical Data Management
Research Technologies
Research Design, Development, & Quality Assurance

5th Floor Blockley Hall
423 Guardian Drive
Philadelphia, PA 19104-6021
CRCU Main Number: 215-573-4422
CRCU Fax: 215-573-1203

Main Contact:
Florence Speiser, M.S.
Senior Manager
215-573-5765
CRCU-Contact@lists.upenn.edu

Faculty Director Contact Information:
J. Richard Landis, Ph.D.
215-573-4922
jrlandis@pennmedicine.upenn.edu

The services offered are given below:
Flow Cytometry Data Analysis Services.
Web-Based Tools For Access.

Identifying and sorting cells from a rapidly moving fluid stream, once as novel an idea as a Wright Brothers plane, has been possible for more than four decades. However, where earlier technology was esoteric, complicated and not widely used, facilities such as the Flow Cytometry and Cell Sorting Resource Laboratory have helped to make this technology widely accessible and relatively easy to use. New multiparametric techniques using sensitive fluorescent probes, now available in a multitude of colors, make cell sorting and analysis (flow cytometry) a rapid, accurate and objective method to measure multiple characteristics of large numbers of individual cells simultaneously.
One of the Resource lab's primary missions is teaching this technology, consulting with investigators regarding integration of this technology into their research paradigms, and providing technical support to regular users.

Flow Cytometry and Cell Sorting Resource Laboratory
297 John Morgan Building
(Temporarily 202 and/or 206 John Morgan Building)
3620 Hamilton Walk
Philadelphia, PA 19104-6082

Contact Information:
Hank Pletcher,
Technical Director
Phone:215-898-3528,
email: pletcher@pennmedicine.upenn.edu

Core Director:
Jonni S. Moore, Ph.D.
215-898-6853
moorej@pennmedicine.upenn.edu

Core staff will educate and assist scientists with HTS assay development, optimization, miniaturization, and validation; maintain libraries of siRNA, shRNA, cDNA, and FDA approved/FDA-like organic small molecule libraries for HTS; and provide robotics infrastructure and technically trained staff for HTS, including small screens of user defined libraries. The High-throughput Screening core also provides direct assistance with preparation of grant applications by drafting experimental designs approaches and providing Letters of Support, offering HTS resources and analysis expertise for the proposed research.

Services Include:
HTS assay development consultation
Automated laboratory robotics and usage training
Small scale screens of user defined libraries (e.g. kinome)
Large scale screens (e.g. whole genome, diversity sets)
HTS Data analysis and data management
HTS reagents (i.e. transfection reagents, micro-titer plates, tips)
Chemical screening (FDA, FDA-likes, synergy, etc)
Genetic screening (siRNAs, shRNAs, cDNAs)
Grant support

Contact Information:
Sara Cherry, Ph. D.
Scientific Director
(215) 746-2384
cherrys@pennmedicine.upenn.edu

David C. Schultz, Ph.D.
Technical Director
215-573-9641
dschultz@pennmedicine.upenn.edu

The services offered are given below:
Experiment Design - Advice on techniques, sequencing depth, and analysis.
Sample Quality Assessments - Agilent bioAnalyzer and TapeStation, Life quBit, KAPA Library Quant kit
Library Preparation - Various protocols for Illumina sequencing.
Illumina hiSeq sequencing - 50bp and 100bp, single-read and paired-end
Illumina miSeq sequencing - 50 to 500bp total, single-read and paired-end
Data Analysis - Basic and custom (FGC only) analysis for microarray and sequencing data.
Microarrays (FGC only) - Agilent microarrays for RNA expression experiments.

More information on their facilities, schedule and people involved can be found on their homepage.

Location:
12-160 Smilow Center for Translational Research,
3400 Civic Center Blvd. Bldg. 421
Philadelphia, PA 19104-5156

Contact:
Klaus Kaestner
Director
215-898-8759
kaestner@pennmedicine.upenn.edu

Jonathan Schug
Technical Director
215-898-0773
jschug@upenn.edu

The services offered are given below:

Sequencing Services:
Sanger Sequencing on ABI 3730

NGS (Next-Generation Sequencing) on Ion
Torrent PGM and S5 & Proton

Size Selection (Pippin Prep) & DNA/RNA QC
for NGS libraries

AMPure Bead Purification of Amplicons and
DNA Fragments

DNA and RNA analysis on Agilent 2100
Bioanalyzer

Other Services:
Genotyping and Fragment Analysis Services

Molecular Biological Services

Bioinformatics

Please visit the DNA Sequencing homepage to learn more about the services that they offer.

The available software, forms and pricing information are available under the "Resources" section of the homepage. The contact details are given below:

Mailing Address:
502 Stellar Chance Labs
422 Curie Boulevard
Philadelphia, PA 19104

E-mail: dnaseq@mail.med.upenn.edu
Phone: 215-573-7407
FAX: 215-573-9327

Tapan Ganguly, Ph.D, Director
(215) 573-7238

The services offered are given below:
Consultation
Data Management
Programming
Dataset Analysis
Data Storage
Software and Analysis Support
Website Hosting
Workstation Use
microRNA profiling,
epigenetic DNA assays, and
translational molecular diagnostics for clinical research

Location:
57 John Morgan Bldg. Basement
3620 Hamilton Walk
Philadelphia, PA 19104-6082
phone: 215-573-6316

Core Director:
Tapan Ganguly, Ph.D.
phone: 215-573-7238
gangulyt@pennmedicine.upenn.edu

Technical Director:
John Tobias, PhD
215-573-4791
jtobias@pennmedicine.upenn.edu