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Host-Microbial Analytic and Repository Core (H-MARC)

Gary Wu, MD

Image Analysis and Gene Expression Quantification Core    Technical Director                                                                     Lillian Chau, MS                                                                  Technical Assistant                                                                    Erika Panfen

Microbial Culture and Metabolomics Core                                 Technical Director                                                                     Elliot Friedman, PhD                                                           Technical Assistant                                                                           Erika Panfen

Lab: 933 BRB II/III
Phone: 215-573-9571
Fax: 215-573-2024

The mission of H-MARC is to provide services that will enhance the analysis of both host and microbial biological processes as well as facilitate translation into the clinical arena via human subject research.

Equipment Reservation and Sign-Out

Click here to reserve PCR instruments and loan-out items

Image Analysis and Gene Expression Core                             A number of analytic instruments to qualify and characterize gene expression are available for use.  Reservations may be required (see above).  Additionally, the Core subsidizes the cost of specific Penn-based technical services to assist Center members in their research projects.

Equipment available in room 933 BRB II/III for use by all Center Members:

  • ABI 7000 Sequence Detection System, $25/plate
  • ABI StepOne Plus Real-Time PCR System, $25/plate
  • Agilent Bioanalyzer (Penn’s Microarray Facility)
  • Becton Dickinson Accuri C6 Flowcytometer
  • BioRad Gel Doc XR+ Imaging System
  • Molecular Dynmaics 840 Phosphoimager
  • Odyssey Infrared Imaging System (Li-Cor) $25/use
  • Promega GloMax Multi Detection System
  • Thermo Scientific Nanodrop 2000 Spectrophotometer

Ancillary equipment available:

  • Thermal Cycler (ABI 2720)
  • Dissecting Microscope (Olympus)
  • Seven -80C Freezers with wireless alarm monitoring
  • Polytron PT-10-35 Homogenizer

Software available:

  • MacVector 7.0
  • Lasergene 5.0
  • Prism 4/6 (Graphpad)
  • Chenomx NMR Suite

Microbial Culture and Metabolomics Core

The Microbial Culture and Metabolomics Core features facilities and equipment for the aerobic and anaerobic culture of microbial species in both batch and continuous systems as well as services for both targeted and untargeted metabolomics. The core offers training and usage for all equipment as well as consultation towards experimental design and method development of microbial culture studies. Additionally, the core offers anaerobic culture services. 

Equipment and Services Available:

  • Anaerobic Chamber (Type B, Coy Labs)
  • Automated Biorector (BioFlo 320, Eppendorf)
  • Waters Acquity uPLC System with a QDa single quadropole mass detector


  • Targeted Metabolomics – bile acids, short chain fatty acids, amino acids, $40/each or  $80/all
  • Untargeted metabolomics with Metabolon, 5% Discount

Genomic Services                                                            Services provided by the Penn Next Generation Sequencing Core and the Penn Molecular Profiling Facility are subsidized by the Core, $1000/investigator/year.

Penn Next Generation Sequencing Core http://www.med.upenn.edu/cores/NextGenerationSequencingCore.html

Director                                                                                       Karl Kaestner, PhD                                                                    215-898-8759                                                                    Technical Director                                                                 Jonathan Schug, PhD                                                                215-898-0773

Biostatistics and Bioinformatics                                Biostatistical support for the development of study design and data analysis is available through the Penn Center for Clinical Epidemiology and Biostatistics (CCEB).

Biostatistician                                                                                Amy Praestgaard, MS 

Bioinformatics                                                                                 Customized bioinformatic analyses specific to the needs of Project Leaders are available to Center members with a computational biologist with expertise in the analysis of host-microbial interactions through the Penn Center for Clinical Epidemiology and Biostatistics (CCEB).

Director                                                                                Hongzhe Li, PhD                                                                        215-573-7238

Computational Biologist                                                                Yun Li, PhD                                                                                215-746-5432

Human 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 and tracked with 2-D barcodes logged into the LabVantage Laboratory Information Management System (LIMS).


University of Pennsylvania | Perelman School of Medicine