Metabolic Phenotyping Core

Human based nutrition and obesity research studies are generating data at an unparalleled pace. These data permit investigators to generate many disease-related hypotheses; however the sophisticated infrastructure needed to create disease-relevant models and the detailed metabolic technologies necessary to test these hypotheses lie outside the expertise of many individual research groups. Core Director Alex Soukas’s recent work in Cell, describing two metformin response elements, conserved from worms to humans, through which metformin inhibits cancer growth and prolongs lifespan exemplifies the type of translational work supported by this Core.

The goal of the Metabolic Phenotyping Core is to provide users with access to high-quality model creation and detailed metabolic phenotyping.

Primary Contact: Alex Soukas

Core Leadership

Alexander Soukas, MD, PhD

Alexander Soukas, MD, PhD

Co-Director of Metabolic Phenotyping Core
Assistant Professor of Medicine
Massachusetts General Hospital, Center for Human Genetic Research
CPZN6224, 185 Cambridge St.
Boston, MA  02114

Robert Gerszten

Robert Gerszten

Co-Director of Metabolic Phenotyping Core
Herman Dana Professor of Medicine
Beth Israel Deaconess Medical Center
330 Brookline Ave.
Boston, MA  02215
Phone: 617-661-7000



  • Assistance with selecting appropriate methods to translate concept into hypothesis-testing research
  • Guidance on study design and methods to incorporate available Core techniques into grants and protocols.

Model Generation

  • siRNA gene knockdown
  • shRNA lentiviral gene knockdown
  • Lentiviral gene overexpression
  • Primary hepatocyte cell culture
  • Immortalized cell culture
  • iPS-derived hepatocyte/adipocyte differentiation

Metabolic Phenotyping

  • Metabolomics
  • GC-MS fatty acid profiling/chromatography
  • mRNA and protein sample preparation
  • Targeted metabolic gene expression
  • Biochemical insulin signaling assay
  • Hepatocyte glucose output and lipolysis assays
  • Seahorse mitochondrial assays
  • Murine body composition analysis
  • Murine 84h energy expenditure


Echo-MRI 100H

Sable Promethion 16-cage indirect calorimetry apparatus
XF24 and XF96 Seahourse Analyzers
Nikon SMZ800 dissecting microscopes
Nikon SMZ1500 dissecting microscope equipped with a UV light source for fluorescence microscopy with a mounted Canon Vixia HF M52 HD video camera
Zeiss Axioobserver A1 inverted microscope with micromanipulators for microinjection
MT Infors incubator for growth
6-channel Clark electrode apparatus for oximetry and energy consumption measurements
Thermo Forma 3110 CO2 water jacketed tissue culture incubators
Zeiss inverted fluorescent microscope
Thermo RT1 refrigerated centrifuge outfitted with aerosol-resistant buckets.
High-throughput screening infrastructure capable of conducting fully automated measurement of morphological and fluorescently detected cellular phenotypes. (Fluorescence Leica DM6000 upright microscope with a motorized Prior 96-well stage, automated filter turret, automated objective head, high-speed, cooled CCD camera, automated image acquisition and analysis software (MetaMorph) and server-level workstation with RAID data storage)
Agilent 1260/6120 LC-MS system outfitted with a diode array detector, a Supelco 24-channel vacuum solid phase chromatography station for lipid class separation and an Agilent 6890 gas chromatograph mass spectrometer (GC/MS) equipped with a Supelcowax-10 column for detailed fatty acid analysis.
Ultra-high performance Thermo LC-MS/MS instruments
Triple quadrupole LC-MS/MS systems (AB/Sciex 5500, Waters Xevo-TQS, Thermo TSQ Quantiva)
Agilent Bravo robots, 2 of which have AssayMap heads for column work
Thermo Kingfisher 96 robot
Perkin Elmer Janus Automated Workstation.