Host Microbial Analytic and Repository Core (H-MARC)

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. H-MARC provides services to address these specific aims that represent the intersection between the host and their microbes in both preclinical and clinical human subject research for the DDRCC Investigator community: 1) Image Analysis and Gene Expression Quantification Facility; 2) Human Biorepository; 3) Penn Metabolomics Core; 4) Microbial Culture & Metabolomics Core, and; 5) Penn Next Generation Sequencing Core.

Grant Citation

Please cite the Center for Molecular Studies in Digestive and Liver Diseases (P30DK050306) in all publications related to core usage.


Gary Wu, MD –

Core Personnel

Technical Director

Lillian Chau, MS –

Technical Assistant

Lindsay Herman – 

Equipment Reservation and Sign-Out

Click here to reserve PCR instruments and loan-out item or scan the QR Code below.

HMARC Equipment Calendar

Equipment Reservation and Sign-Out

Click here to reserve PCR instruments and loan-out items

Core Services

A number of analytic instruments are available to qualify and characterize gene expression are available for use.  Reservations may be required for specific equipment (see link 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 StepOne Plus Real-Time PCR System, $25/plate
  • Becton Dickinson Accuri C6 Flowcytometer
  • BioRad Gel Doc XR+ Imaging System
  • Odyssey Infrared Imaging System (Li-Cor) $25/use
  • Promega GloMax Multi Detection System
  • Thermo Scientific Nanodrop 2000 Spectrophotometer
  • Thermal Cycler (ABI 2720)
  • Dissecting Microscope (Olympus)
  • Twelve -80°C Freezers with wireless alarm monitoring
  • One -140°C Freezer with wireless alarm monitoring
  • PT-10-35 Homogenizer
  • Sonicator

Software available:

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

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).  The core offers consultations on study design and sample collection, as well as standard operating procedures for collection, aliquoting and archival of biospecimens.

The Metabolomics Core provides expertise to quantitate metabolites in biological samples using liquid chromatography/mass spectrometry. Our mission is to perform the assays and assist in the interpretation of the results. The core is available to the entire Penn research community, external research investigators, and industry

Targeted metabolomics assays are available for the quantitative measurement of a wide variety of metabolites in cellular extracts, plasma, or tissues using liquid chromatography/mass spectrometry. These assays provide crucial information about metabolic pathways involving the three major classes of nutrients:  lipids, carbohydrates, and proteins. Our assays include the quantitation of:

  • Acylcarnitines (products of fatty acid oxidation)
  • Amino Acids (products of fatty acid and amino acid oxidation)
  • Organic acids (TCA cycle intermediates; products of glucose and amino acid oxidation)
  • Malonyl and Acetyl CoA
  • Nucleotides

Director: Chris Petucci, Ph.D.
Phone: 215-898-9765
Location: Smilow TRC 9-196

Faculty Core Advisor: Zoltan P. Arany, M.D., Ph.D.
Location: Smilow TRC 11-106

Faculty Core Advisor: Daniel Kelly, M.D
Location: Smilow TRC 11-122


The Penn Microbial Culture and Metabolomics Core provides aerobic and anaerobic culturing services and targeted metabolomics analysis, as well as consultation towards experimental design, method development, and data analyses.

  • Culture studies include isolation of microbial taxa from mammalian samples; interrogation of the physiology of microbial strains under different conditions (e.g., anaerobic/microaerobic/aerobic, differing nutrient limitations) using isolated strains or strains obtained from culture collections (another service offered by the core); co-culturing of defined microbial consortia to investigate microbe-microbe interactions, and; preparation of microbial products (live bacteria, heat-killed bacteria, bacterial supernatants) from single or defined-mixed microbial cultures for use in mammalian cell culture and/or animal model systems.
  • The metabolomics component of the core provides researchers with targeted metabolomics of amino, bile, and short-chain fatty acids and features a Waters Acquity uPLC System with photodiode and QDa single quadropole mass detectors as well as an autosampler.

If you are interested in working with the Penn Microbial Culture and Metabolomics Core, please visit our iLab storefront to learn more and to submit service requests

  • Equipment and Services Available: Two Anaerobic Chamber (Type B, Coy Labs); Microaerobic Chamber (0.1-20% O2 with 0.1% resolution; Coy Labs); Automated Bioreactor (BioFlo 320, Eppendorf); Custom Built Mini-Bioreactor Array (48 parallel 15-mL bioreactors); Waters Acquity uPLC System with both a Photodiode Detector Array and a QDa single quadropole mass detector, and; a Laser Phosphorimeter for phosphorescent quantification of oxygen levels (PMOD 500, Oxygen Enterprises, LLC.)
  • Culture: We offer a wide range of microbial culturing resources and services that can be tailored to each project. Please contact us to discuss specific projects and pricing.
  • Metabolomics: We offer targeted metabolomics analysis of amino, bile, and short-chain fatty acids in fecal, plasma, and microbial culture supernatant samples. 

For more information on the Microbial Culture and Metabolomics Core click here.

Metabolomics Rates - Calendar Year 2022

(Prices are Per Sample)




Amino Acids



Bile Acids



Short Chain Fatty Acids



Any Two Classes



All Three Classes



Core Personnel

Technical Director - Elliot Friedman, PhD
Technical Assistant - Dillon Curry, M.S

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

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

The NGSC offers ultra-high throughput sequencing services for the PSOM research community. This Core offers library quality assessments, sequencing, and preliminary data analysis for a wide variety of experimental protocols including ChIP-seq, RNA-Seq, HITS-CLIP, miR-Seq, exome capture, and whole genome shotgun bisulfite sequencing. There are limited library preparation services, but the NGSC can advise on library preparation techniques. The Core has four Illumina hiSeq2000s for large-scale sequencing and a MiSeq for sample evaluation or library testing. The NGSC provides the following services: 1) Experiment planning; 2) Training in library preparation; 3) Library quality assessment; 4) Sequencing and scheduling; 5) Data quality assessment; 6) Data sharing; 7) Data analysis services; 8) Data submission to public repositories; 9) Data archiving. The NGSC will provide an initial analysis of sequencing data:



Cost per sample

Analysis provided



Peak calls, list of target genes


$25 plus computing

Expression levels for known genes, exon junctions, coverage



Expression levels tor known miRNAs



Position and intensity of footprints on known transcripts and genome



SNPs and small structural variants


Genomic Services                                                          
Some services provided by the Penn Next Generation Sequencing Core may be subsidized by H-MARC.