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Molecular Biology/Gene Expression Core

Gary Wu, MD

Technical Director
Sue Keilbaugh, PhD

Technical Assistant
Ying-Yu Chen

Lab: 934 BRB II/III
Phone: 215-573-1879
Fax: 215-573-2024

The Molecular Biology/Gene Expression Core maintains a library of digestive and liver reagents, maintains a number of analytic instruments to quantify and characterize gene expression, and subsidizes the cost of specific Penn-based technical services to assist Center members in their research projects.

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Equipment sign-out

Click here to reserve PCR instruments and loan-out items


Digestive Disease Reagent Bank

CDNAs and expression vectors relevant to digestive and liver research provided free of charge to members of the Center for Molecular Studies in Digestive and Liver Disease.

Reagents Available:


Image Analysis and Gene Expression Quantification

Equipment available in room 934 BRB II/III for use by all Center Members.

  • Molecular Dynamics 840 Phosphorimager (in 973 BRB II/III)
  • Agilent Bioanalyzer (in Penn's Microarray Facility)
  • BioRad Gel Doc XR+ Imaging System
  • Becton Dickinson FACSCalibur Flowcytometer (in 973 BRB II/III)
  • Odyssey Infrared Imaging System (Li-Cor)
  • ABI StepOnePlus Real-Time PCR System
  • ABI 7000 Sequence Detection System
  • Promega GloMax Multi Detection System
  • Thermo Scientific Nanodrop 2000 Spectrophotometer

Ancillary equipment available:

  • Thermal Cycler (ABI 2720)
  • Dissecting Microscope (Olympus)
  • Canon CanoScan LIDE90
  • Two -80˚C Freezers

Software available:

  • MacVector 7.0
  • Lasergene 5.0 (DNAStar)
  • Prism (Graphpad Software)
  • Partek Genomics Suite 6.4

Gene Expression Profiling

Penn Microarray Core Facility

Vivianna Van Deerlin, MD, PhD
Interim Scientific Director

Kathakali Addya, PhD
Technical Director

Affimetrix microarrays: credit for hybridization and scanning of up to five Affimetrix microarray chips, and 10% discount on all other services at the Penn Microarray Core. Contact Drs. Vivianna Van Deerlin or Kathakali Addya regarding usage, and the GI Center Administrator to obtain credit or discount.

Quantitative Real-Time PCR: for verifying and quantifying expression patterns of specific genes identified by mircoarray gene profiling. An ABI 7000 Sequence Detection System and a StepOne Plus Real Time PCR System are available in 934 BRB II/III for use by Center Investigators at a cost of $25.00 per run. Please contact the Sue Keilbaugh for more information on the use of these instruments.

Bioinformatics Support

University Bioinformatics Core

John Tobias, PhD

Penn Bioinformatics Core personnel provide consulting to enable investigators to frame research questions in genomics terms through transcriptome profiling and identify bioinformatics solutions to those questions. Core personnel are then available to facilitate these solutions that may involve developing databases and software tools as well as provide training and support in the use of these tools.

Biostatistics Support

Center for Clinical Epidemiology & Biostatistics

Ann Tierney, MS

Center members will now be able to obtain Biostatistical support for the development of study design and data analysis through the CCEB by appointment with Ann Tierney, a Biostatistician in the Penn Center for Clinical Epidemiology and Biostatistics.

Biomarker Facility

Center for Excellence in Environmental Toxicology (CEET)

Ian Blair, PhD

Clememtina A. Mesaros, PhD
Technical Director

The Molecular Biology/Gene Expression Core has established an agreement with the Penn Center of Excellence in EnvironmentalToxicology (CEET) to provide access for Center Investigators to services provided by its Molecular Biomarker Core with a 15% discount for all services. The mission of the Biomarker Facility is to foster the use of sophisticated analytical methodologies to detect biomarkers. Biomarkers can be analyzed in model systems, in vivo and ultimately patient populations. The Molecular Biomarker Core provides diverse analytical services primarily based on LC/MS methodology. Immunologically based assays are developed when required.  A wide range of assays are offered including the quantification of endogenous DNA-adducts, aromatic hydrocarbon-derived adducts, urinary lipids/eicosanoids/isoprostanes, saturated and unsaturated fatty acids, RNA-adducts, plasma estrogens/androgens/steroids, and novel biomarkers, to name a few. 

 Human Sample Biorepository

This biorepository of human digestive tissues has two components, 1) Human RNA Source Bank: A previously established bank of frozen human tissues, many with RNA already isolated, and 2) Annotated Clinical Tissue Bank: Biospecimens with robust clinical metadata from prospectively consented human subjects are archived. 


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