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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 had enhanced services to address these specific aims that represent the intersection between host and their microbes in both preclinical and clinical human subject research for the DDRCC Investigator community: Gene Expression and Molecular Quantification Instrument Facility; 2) Subsidize mammalian genomics services provided by the Penn Next Gen Sequencing Core; 3) the Microbial Culture and Metabolomics Core; 4) the Bioinformatics and Biostatistics Core; 5) the Human Biospecimen Repository, 6) Clinical Metadata Collection and Query services; and 7) the Human Intervention Consulting Service.

Director

Gary Wu, MD – gdwu@pennmedicine.upenn.edu

Core Personnel

Technical Director

Lillian Chau, MS – Lillian.Chau@pennmedicine.upenn.edu

Technical Assistant

Sayaka Ogawa – saogawa@pennmedicine.upenn.edu

Equipment Reservation and Sign-Out

Click here to reserve PCR instruments and loan-out items

Become a Center Member! Click here for application

Image Analysis and Gene Expression Quantification Core

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

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

Penn Metabolomics Core

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

Website: https://www.med.upenn.edu/cvi/metabolomics-core.html

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: 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. Please review further details in the metabolomics user guide.

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

Metabolomis Rates - Calendar Year 2020

(Prices are Per Sample)

Analysis

Academic

Industry

Amino Acids

$50

$75

Bile Acids

$50

$75

Short Chain Fatty Acids

$50

$75

Any Two Classes

$100

$150

All Three Classes

$100

$225

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.

For more information about services, pricing, and protocols, please download the following guide.

Core Personnel

Technical Director - Elliot Friedman, PhD
                                                          
Technical Assistant - Dillan Murphy

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

Penn Next Generation Sequencing Core

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

https://ngsc.med.upenn.edu/#/

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:

 

Technique

Cost per sample

Analysis provided

ChIP-Seq

$25

Peak calls, list of target genes

RNA-Seq

$25 plus computing

Expression levels for known genes, exon junctions, coverage

mi-Seq

$25

Expression levels tor known miRNAs

HITS-CLIP

$25

Position and intensity of footprints on known transcripts and genome

Exome-Seq

$100

SNPs and small structural variants

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