Host Microbial Analytic and Repository Core (H-MARC)

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 939A BRB II/III for use by Center Members:

• QuantStudio3 qPCR Machine, $25/plate
• BioRad Gel Doc XR+ Imaging System
• Odyssey Infrared Imaging System (Li-Cor) $25/use
• Promega GloMax Multi Detection System
• Varioskan LUX Multimode Microplate Reader
• Thermo Scientific Nanodrop 2000 Spectrophotometer
• Thermal Cycler (ABI 2720)
• Dissecting Microscope (Olympus)
• Twelve -80°C Freezers with wireless alarm monitoring
• One Cryostorage Freezer with wireless alarm monitoring
• PT-10-35 Homogenizer
• Sonicator

Software available:

• Ingenuity
• Prism 10 (Graphpad)
• PrimerExpress

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 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.

(Prices are Per Sample)

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

H-MARC provides a subsidy for services provided by the Penn Genomics and Sequencing Core (PGSC).

The Penn Genomics and Sequencing Core (PGSC) provides a spectrum of sequencing, genomics and molecular biological services with a team of highly experienced and trained professionals under a Director and Technical Director. The services include consultation on experimental design to performing experiment to downstream data analyses.

Next-Generation Sequencing on multiple platforms:

Short Read - Illumina NovaSeq X Plus, NextSeq 2000 and MiSeq

Long Read - PacBio Revio and Oxford Nanopore MinION

This includes DNA/RNA extraction from different sources, library preparation with quality control, and sequencing followed by bioinformatics.

Applications include mRNA-Seq, total RNA-Seq, small RNA-Seq, WGS, targeted sequencing, ChIP-Seq on X Plus; WGS and whole methylome on PacBio etc.

For single-cell genomics we use 10X Genomics Controller; the applications include scRNA-Seq and snRNA-Seq. Soon we are going to introduce multiplexed scRNA-Seq. Multiome including scATAC-Seq are under development.

Bioinformatics support is available for both core and externally generated datasets.

Legacy Sequencing: Sanger Sequencing on ABI 3730xl capillary sequencer.

The capillary sequencer enables fragment analysis for microsatellite-based genotyping, human cell line authentication and other applications.

Targeted molecular profiling including genotyping and gene expression is performed using ThermoFisher QS6 Pro and Qiagen digital PCR instruments. Mouse genotyping is done using PCR-based approach.

For further information, please contact Director, Tapan Ganguly, gangulyt@pennmedicine.upenn.edu and Technical Director, Erik Toorens, toorens@pennmedicine.upenn.edu.

Sample Drop-off Hours and Location

11:00AM-12:00PM - Tuesday to Thursday

2:30PM - 3:30PM - Monday to Friday

Charges for Major NGS Services

H-MARC provides a subsidy for services provided by the 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