Facility Information for Grant Applications
The Research Technology Support Facility (RTSF) at Michigan State University is supported and managed under the auspices of the Office of Research & Innovation. RTSF Cores provide technical and analytical support for Biomedical, Agricultural, and Engineering research.
The MSU Genomics Core operates in approximately 3,000 sq. ft. of lab space and provides many types of DNA and RNA sequencing services to both MSU researchers and the wider research community. Equipment within the Core includes an Element Biosciences AVITI and an AVITI24 for next-generation short-read sequencing. A 10X Genomics Chromium X is used to generate single cell sequencing libraries, and a 10X Genomics CytAssist is used to prepare Visium spatial transcriptomics libraries. Three Oxford Nanopore PromethION P2 instruments are available for long-read DNA, cDNA and direct RNA sequencing. Size-specific shearing of nucleic acids is achieved with a Covaris M220 Sonicator. Two Agilent 4200 TapeStations are used for RNA and DNA quality and size analysis. A Pippin Prep from Sage Science allows gel-based size selection and clean-up of short-read sequencing libraries. Fluorescence-based nucleic acid quantification is performed on Invitrogen Qubit and Qubit Flex devices.
Mass Spectrometry and Metabolomics Core
The Mass Spectrometry and Metabolomics Core is an open access resource where researchers and facility staff perform small molecule, macromolecule, and metabolomic analyses using 12 mass spectrometers. The Core is located in 3,400 sq. ft. of laboratory space (newly renovated in 2023) in the basement of the Biochemistry Building (Rooms 11, 15, 17). Core staff provide training in experiment design, theory and operation of instruments, method development, and data interpretation. Trained instrument users enjoy 24/7 open access for instrument use and hourly or per-sample fees are charged based on the instrument. The facility houses three GC/MS systems: one single quadrupole GC/MS (Agilent 5975C, equipped with a CTC PAL autosampler as well as a Teledyne AtomX XYZ purge-and-trap accessory), one triple quadrupole GC/MS/MS instrument (Agilent 7010B equipped with a CTC PAL autosampler and capabilities for headspace analysis and a Chromtech TDAS 2000 system for thermal desorption analysis) and one GC-Time-Of-Flight MS (Leco GC-HRT+) capable of providing accurate mass measurements. There are a total of 8 LC/MS/MS instruments: four triple quadrupole LC/MS/MS systems (Waters Xevo TQ-XS, Xevo TQ-S micro, Xevo TQ-S, and Xevo TQ Absolute XR), one Thermo Q-Exactive LC/MS/MS, two Waters Xevo G2-XS QTof LC/MS/MS systems and a Sciex ZenoTof 7600 LC/MS/MS. The core also houses a Bruker ultrafleXtreme MALDI-TOF/TOF with imaging capabilities and an HTX M3+ sprayer for MALDI imaging sample prep. A Waters eλ photodiode array detector is configured on one of the QTof LC/MS/MS instruments. All mass spectrometers are equipped with autosamplers, and all of the LC/MS instruments are interfaced to UHPLC pumps. Untargeted processing of LC/MS data is achieved using Waters Progenesis QI and Thermo Compound Discoverer software, and Agilent Profiler and MassProfiler Professional (MPP) software is used for untargeted analysis of GC/MS data. Software for MALDI data analysis includes SCiLS Lab (imaging data) and PolyTools (polymer data).
The Proteomics Core has at its disposal two state-of-the-art LC/MS/MS mass spectrometers; a Thermo Scientific Q-Exactive interfaced with a Thermo Scientific EASY nLC 1200 UPLC and a Thermo Scientific Excedion Pro with extended mass range and EASY EThcD capabilities interfaced with a Thermo Scientific Vanquish NEO UPLC, both with Flex-Spray Ionization Sources. These systems combine unique High Resolution/Accurate Mass measurement and high sensitivity Orbitrap detection with exceptional mass selection and spectral multiplexing over extended, stable LC gradients making them ideal for proteome profiling of complex samples and highly specific peptide quantitation. Deep proteome mapping can be achieved using a Waters Acquity H-class UPLC for offline MUDPIT-style analyses. Software assets include Mascot Distiller, Proteome Discoverer, MaxQuant, Skyline and Scaffold software suites. Mascot, SEQUEST, MSFragger and Andromeda search algorithms are available for peptide-to-spectrum matching and quantitation.
The Cryo-EM Facility provides state-of-the-art instrumentation and computational infrastructure to support high-resolution structural biology and cellular imaging studies. The facility houses two transmission electron microscopes and one focused ion beam scanning electron microscope optimized for cryo-electron microscopy and tomography applications. The facility includes a ThermoFisher Talos Arctica, a 200 kV field emission transmission electron microscope designed for grid and sample screening to optimize high-resolution structural studies. The instrument is equipped with a Falcon 4i direct electron detector and Selectris Energy Filter and is supported by EPU and Tomo software packages. In addition, the facility houses a ThermoFisher Titan Krios G4i, a 300 kV field emission transmission electron microscope routinely capable of generating structures at resolutions better than 2 Å. The Krios is equipped with a Falcon 4i camera and SelectrisX Energy Filter and is supported by EPU, Tomo, and EPUD software packages. The facility also maintains a ThermoFisher Helios Hydra Bio FIB-SEM, which utilizes an inductively coupled plasma ion source with four ion options (Xenon, Argon, Nitrogen, and Oxygen). The Hydra is equipped with an integrated fluorescence light microscope correlative system (iFLM) and an Easylift nanomanipulator for cryo-lift-out workflows.
The Cryo-EM Facility provides a comprehensive suite of biological sample preparation instrumentation, including a Leica ACE600 carbon evaporator; ThermoFisher Vitrobot Mark IV and Leica GP2 robotic plunge-freezing systems; Pelco EasyGlow and GoQube Plus glow discharge units; a Precisionary Compresstome VF-510-0Z tissue sectioning instrument; and a CryoCapCell high-pressure freezer. Long-term cryogenic sample preservation is supported through dedicated Subangstrom storage dewars for grid and planchette storage.
Computational resources include access to a dedicated DDN Solutions data storage system with a capacity exceeding 1 PB for long-term archival and management of cryo-EM datasets. Data acquired from all microscopes are transferred to users through Globus. In addition, investigators have access to dedicated GPU-enabled computational workstations located in the Biochemistry Building at Michigan State University. These systems are pre-configured with cryo-EM reconstruction and analysis software packages including CryoSPARC, RELION, IMOD, and AreTOMO.
Metabolic Phenotyping & Preclinical Imaging (MPPI) Core
The Metabolic Phenotyping & Preclinical Imaging (MMPI) Core at Michigan State University provides support for preclinical research in metabolic disease, cancer, and aging through advanced in vivo optical imaging and metabolic phenotyping platforms, including the IVIS Spectrum, TSE PhenoMaster NG system, Bruker LF90II, and X-RAD320. Our experienced staff provide experimental design consultation, training, and full-service support to ensure rigor, reproducibility, and compliance with institutional and regulatory guidelines.
The IVIS Spectrum Imaging System located in room 1117 (194 sq. ft.) of the Biomedical Physical Science building (BPS) enables non-invasive, longitudinal in vivo imaging of disease progression, cel trafficking, and gene expression. The system features integrated isoflurane anesthesia, a heated stage and a 5-position a manifold for high-throughput imaging (up to 5 mice simultaneously). The Imaging Wizard guides the user through imaging set-up and acquisition. Multispectral excitation/emission filters and advanced spectral unmixing algorithms support detection of multiple bioluminescent and fluorescent reporters from visible to near-infrared wavelengths. Living Image software enables 3D reconstruction and quantitative analysis with anatomical co-registration with the digital “mouse atlas” (or other imaging modalities) An adjoining room (286 sq. ft.) provides sterile IVC animal housing using the Optimice System, two (6ft. NuAire, and 4ft. Labconco Purifier Logic) Class II Type A2 Biosafety cabinets, a Nikon SMZ-745T Stereo Microscope with Nikon color digital camera for live image capture, and benchtop (isoflurane) anesthesia machine for animal manipulations/procedures.
The X-RAD320 Biological Irradiator is located in a controlled access space, room 1114 (191 sq. ft.) in the Biomedical Physical Science Building (BPS). The X-RAD320 is a cabinet-style X-ray system designed for precise reproducible irradiation of small animals, cells, and biological samples. It operates at energies up to 320 kVp and is equipped with adjustable dose rates, beam filtration options, and programmable exposure settings, allowing investigators to tailor irradiation protocols to specific experimental needs. The X-RAD320 supports diverse experimental applications, including preconditioning for bone marrow transplantation, tumor irradiation, radiation-dose response curves, immune and hematopoietic system modulation, radiation injury, and tissue repair models.
The TSE PhenoMaster NG system located in the Interdisciplinary Science and Technology Building (ISTB) vivarium, is an advanced, modular metabolic phenotyping platform designed for comprehensive assessment of energy balance, activity, and feeding behavior in mice. This platform enables continuous, high-resolution metabolic measurements under controlled environmental conditions. Key capabilities include indirect calorimetry (measurement of VO2, VCO2, RER and Energy Expenditure); ingestive behavior (real-time food and water intake, meal pattern analysis); locomotor activity monitoring spontaneous activity, voluntary running wheel activity). The PhenoMaster NG platform supports long-term, continuous data acquisition, allowing detailed assessment of metabolic phenotyping across circadian cycles under minimally stressful conditions. Core staff provide full-service study execution, including system calibration, animal handling and monitoring, and data preparation for analysis by investigators.
The Bruker Minispec LF90II Body Composition Analyzer, located in the ISTB vivarium, utilizes time-domain nuclear magnetic resonance (TD-NMR) technology for rapid, non-invasive, quantitative, longitudinal assessment of body composition (lean tissue, fat, and fluid), which is essential for studies of energy balance, metabolic disease, and treatment response. Its non-invasive nature allows repeated measurements in the same conscious animals over time, reducing variability, and animal use while increasing statistical power.
In Vivo Study Support Services – with over 30 years’ experience in the care and use of laboratory animals (particularly mice) in research, core personnel provide comprehensive animal study support services to ensure rigorous, reproducible, and compliant in vivo research. Services include experimental design consultation, IACUC protocol development, and full-service execution of animal studies including mouse colony management, compound administration, tumor modeling, irradiation procedures, necropsy, and tissue collection. These services are particularly helpful to investigators with limited in vivo experience or without dedicated technical personnel. Core personnel can provide hands-on training/guidance, or perform all animal procedures in accordance with IACUC, and AAALAC standards to ensure animal welfare and high-quality data generation.
Transgenic & Genome Editing Facility
The Transgenic & Genome Editing Facility (TGEF) provides faculty with comprehensive expertise, resources, and support in genetic engineering, molecular cloning, and genome editing. The mission of TGEF is to support the in-house generation of transgenic organisms, embryos and cells in a variety of species using the latest genome editing technologies such as CRISPR-Cas. TGEF provides support at all stages of genome editing projects, including project consultation and grant preparation, experimental design, construct generation, validation and molecular screening, and delivery of genome editing reagents to cells and embryos through transfection, electroporation or microinjection. TGEF supports mouse and rat models for routine genome editing but consults on and develops CRISPR editing in other species used by faculty on campus, including other rodents, large animals, fish, and insects. Editing of cell lines is supported through consultation, reagent design, and PI collaborations. TGEF also offers expert guidance in breeding strategy and colony maintenance, procurement and importation of roden lines, and rederivation, cryopreservation, and cryo-recovery of rodent strains.
The Stem Cell Core (SCC), located in the Bio Engineering Building at the MSU East Lansing South Campus, provides comprehensive expertise, resources, and support for basic and translational research. The core's primary mission is to advance the in-house adoption of stem cell approaches, providing a faculty with a full suite of services. These specialized services include somatic cell reprogramming to induced pluripotent stem cells (iPSCs) from PBMCs or fibroblasts using episomal, Sendai virus, lentiviral, or RNA platforms; CRISPR RNP-based gene editing for knockouts and small modifications; organoid and assembloid culture system development; cryo-banking of stem cell lines; and hands-on human iPSC culture and methods training.
To support these workflows, the SCC tissue culture facility houses two 5-ft Biosafety Cabinets (Thermo, 1300 series) and two stacked Thermo Heracell Vios 160i CO2 incubators with copper interiors, and access to a Heracell incubator with oxygen regulation 1%-21% Thermo incubator at the Aguirre lab. The core has a Leica DMi8 tissue culture microscope equipped with an object marker cell objective, and a digital inverted microscope EVOS XL Core with 4x, 10x and 20x Achro/PH Objectives, dedicated to clone picking. A, Neon NxT eukaryotic cell electroporator/nucleofector (Thermo Fisher) is available for delivery of nucleic acids to iPSCs and cell lines. Moxi Z Mini Automated Cell Counter (ORFLO Technologies) and an EVE cell counter (NanoEntek) are available for cell density quantification. Sample preservation and cold storage infrastructure consists of an Eppendorf CryoCube -80°C high-performance freezer, a VWR frosted -20°C freezer, a Thermo CryoPlus 1 liquid nitrogen (LN2) storage system, and a VWR CryoPro LN2 storage system.
For imaging and characterization of iPSC and organoids, the SCC core partners with the IQ microscopy core, Flow Cytometry Core and other shared resource cores on campus to get access to confocal, light sheet and spinning disk confocal and flow cytometry instruments.
Additional Core Facility Grant Support Documentation: