Molecular Biology/Gene Expression Core
Director
Gary Wu, M.D.
Technical Director
Sue Keilbaugh, Ph.D.
Technical Assistant
Ying-Yu Chen
Lab: 630 CRB
Phone: 215-573-1879
Fax: 215-573-2024
- Center Member Application (Word doc)
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.
Acrobat Reader needed to view or print reagent summary and detail, and order forms.
Equipment sign-out
Click here to reserve PCR instruments and loan-out itemsServices
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:
Reagent:
- Order Form (pdf)
- Donations to core for shared use (pdf)
Image Analysis and Gene Expression Quantification
Equipment available in room 630 CRB for use by all Center Members.
- Molecular Dynamics 840 Phosphorimager
- Agilent Bioanalyzer (in Penn's Microarray Facility)
- BioRad Universal Hood (ChemiDoc)
- Becton Dickinson FACSCalibur Flowcytometer
- Odyssey Infrared Imaging System (Li-Cor)
- Real-Time PCR System (Step-One Plus, ABI)
- Promega GloMax Multi Detection System
Ancillary equipment available:
- Thermal Cycler (ABI 2720)
- Z1 Coulter Particle Counter (Beckman Coulter)
- Dissecting Microscope (Olympus)
- Canon CanoScan LIDE90
- Two -80˚C Freezers (Thermo Fisher ULT2586-10-D43)
Software available:
- MacVector 7.0/DNAstar
- Lasergene 5.0 (DNAStar)
- Prism (Graphpad Software)
- Partek Genomics Suite 6.4
- Ingenuity Pathway Analysis
Gene Expression Profiling
Penn Microarray Core Facility
http://www.med.upenn.edu/bmcrc/microarr/?microarr)
Don Baldwin, Ph.D., Director
Tel: 215-898-3675
e-mail: dbaldwin@mail.med.upenn.edu
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 Don Baldwin, PhD 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 630 CRB 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
http://www.bioinformatics.upenn.edu
John Tobias, PhD Tel: (215) 573-4791
email: jtobias@pcbi.upenn.edu
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
http://www.cceb.upenn.edu
Ann Tierney, MS Tel: (215) 573-3934
email: atier@mail.med.upenn.edu
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, Ph.D., Director
Tel: (215) 573-9880
e-mail: ianblair@mail.med.upenn.edu
Clememtina A. Mesaros, Ph.D., Technical Director
Tel: 215-573-9878
e-mail: mesaros@upenn.edu
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.
Clinical Metadata Collection and Query – not available as yet
The Core is initiating a collaboration with the Children’s Hospital of Philadelphia (CHOP) to utilize the EPIC electronic medical record to collect patient-specific clinical metadata that can then be downloaded and queried through the Penn Health System’s data warehouse known as the Penn Data Store (PDS).