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Resource 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 the Vice President for Research and Graduate Studies.

The RTSF Cores provide technical and analytical support for Biomedical and Agricultural research at Michigan State University in Flow Cytometry, Genomics, Mass Spectrometry and Metabolomics, Cryo-electron Microscopy, Research Greenhouses, and Proteomics. The Flow Cytometry Core offers two multiple laser-based optical flow cytometers that analyze cell populations for multiple characteristics simultaneously. The Genomics Core provides single gene to genomic scale DNA sequencing services, fragment analysis genotyping, qPCR, and other nucleic acid QC services. The Proteomics Core offers high-throughput mass spectral protein identification and determination of protein expression patterns. The Mass Spectrometry and Metabolomics Core uses an array of mass spectral techniques for small molecule identification as well as analyses and for Metabolomic profiling.

 

Flow Cytometry Core

The Flow Cytometry Core is no longer a part of RTSF, but has merged with the MSU Flow Cytometry Core Facility. For more information please visit their website here

 

Genomics Core

The MSU Genomics Core provides small scale to genome size high throughput sequencing services. The Core also provides instrumentation for SNP profiling, fragment analysis genotyping, Quantitative Real Time PCR and other nucleic acid QC services. Equipment within the Core includes an Illumina HiSeq 4000, an Illumina NextSeq 500 and two Illumina MiSeqs for next-generation sequencing. An Oxford Nanopore GridION is available for long-read sequencing, and an Oxford Nanopore PromethION is expected to be introduced to the Core in late November 2019. An ABI 3730xl 96-capillary DNA sequencer performs traditional Sanger sequencing, fragment analysis and SNP sequencing. A TakaraBio SmartChip RT-PCR System and an Applied Biosystems QuantStudio 7 Flex are used for qPCR analysis. Gene expression analysis may also be performed on a NanoString nCounter. A Biomek FX robot and a BioMek 3000 robot are available for repetitive liquid handling tasks. Size-specific shearing of nucleic acids is achieved with a Covaris M220 Sonicator. An Agilent 4200 TapeStation and an Agilent 2100 Bioanalyzer are used for RNA and DNA quality and size analysis. Fluorescence-based nucleic acid quantification is performed on either an Invitrogen Qubit or a FLUOstar OPTIMA plate reader.

 

Mass Spectrometry and Metabolomics Core

The RTSF Mass Spectrometry and Metabolomics Core is an open access resource where MSU researchers and facility staff perform analyses of small molecules, intact macromolecules, peptides, lipids, and metabolomic analyses using 12 mass spectrometers. Analyses typically involve compound identification or quantitative analysis.  Students and other researchers are encouraged to become certified users of the instruments, and the facility staff offers frequent training in the theory and operation of facility instruments. Trained instrument users enjoy 24/7 open access to instruments; four staff experts perform analyses and provide consulting regarding method development and data interpretation. The facility houses seven LC/MS/MS instruments including Waters Xevo TQ-S, Quattro Premier XE, Acquity TQ-D, and Quattro Micro API UPLC/MS/MS systems, all of which are tandem quadrupole systems dedicated to targeted analysis of small molecules. The complement of LC/MS/MS instruments offers analyses using electrospray, atmospheric pressure chemical ionization (APCI), nanoelectrospray, and atmospheric pressure photoionization (APPI). In addition, two Waters Xevo G2-XS QTof UPLC/MS/MS systems and a Thermo Q-Exactive UPLC/MS/MS instrument provide accurate mass (high resolution) analyses of synthetic and natural products, non-targeted and targeted metabolomic, lipidomic, and glycomic profiling, and analyses of peptides and intact macromolecules including hydrogen/deuterium exchange (HDX). Four GC/MS instruments are also available including Agilent 5975C and Thermo DSQ-II quadrupole GC/MS systems, an Agilent 7010B tandem quadrupole GC/MS/MS system, and a Waters GCT Premier GC/TOF high resolution MS instrument. GC/MS and MS/MS capabilities include EI and CI, automated SPME injections, and thermal desorption analysis. MALDI analyses of materials ranging from small molecules, peptides, oligonucleotides, metabolites, and polymers can be performed on a Shimadzu AXIMA-cfr plus instrument equipped with MALDI imaging capability. Metabolomic and metabolite profiling analyses can be performed using a variety of instrument platforms, and are supported with data processing and statistical analysis software. Methods are currently running for high-throughput LC/MS/MS profiling of amino acids, phytohormones, signaling oxylipins, structural lipids, and organic acid metabolites. The Core performs analyses of approximately 40,000 samples/year from institutions from around the world.

 

Proteomics Core

The Proteomics Core has at its disposal two state of the art LC/MS/MS mass spectrometers; a Thermo Scientific Q-Exactive and a Thermo Scientific Linear Ion-Trap (LTQ).  The Q-Exactive is interfaced with a Thermo EASY nLC-1000 UPLC and Flex-Spray Ionization Source.  Together this system combines unique High Resolution/Accurate Mass measurement capabilities and high sensitivity Orbitrap detection with exceptional mass selection and spectral multiplexing over extended, stable LC gradients making it ideal for deep proteome profiling of complex samples and highly specific peptide quantitation.  The LTQ is connected to a Waters nano-Acquity UPLC and offers high sensitivity, rapid scanning speed and MSn capabilities along with exceptional chromatographic separation.  The facility offers data processing and quantitation using Mascot Distiller, Proteome Discoverer, MaxQuant and Skyline software suites.  Mascot, SEQUEST and Andromeda search algorithms are available for peptide-to-spectrum matching as well as Scaffold for data visualization and statistical validation.  Up front chromatographic fractionation of complex peptide samples is offered using a Waters Acquity H-class UPLC and an Agilent 3100 Offgel Fractionator.  Protein level separation can be performed using the Invitrogen ZOOM IEF fractionator or with 1D and 2D PAGE.

 

Research Greenhouse Complex Core

The MSU Plant Science Research Greenhouse Facility is comprised of 130 individual greenhouse sections totaling approximately 92,000 square feet on main campus, as well as 12 greenhouse sections totaling approximately 22,000 square feet on the south campus farms. The main campus greenhouses are located on the southeast corner of Farm Lane and Wilson Road, and can be accessed from five surrounding buildings via underground tunnels, allowing for movement of plants between greenhouses and labs without exposing plants to cold temperatures in winter. Several sizes of plastic pots, potting media, and field soil are supplied, as well as one slow release fertilizer and one water soluble fertilizer. The facility's pesticide coordinator is available for scouting and pesticide application (pesticides are provided by the facility) as necessary.

 

IVIS Spectrum Imaging Core

The IVIS Spectrum is a versatile, advanced in vivo bioluminescent and fluorescent pre-clinical imaging system that combines high-throughput (image up to 5 mice, or 2 rats at a time) and full tomographic optical imaging in one platform. The light tight imaging chamber with heated stage and integrated gas anesthesia (isoflurane) allows for non-invasive sequentially imaging over time yielding valuable information on disease progression, cell trafficking and gene expression patterns in living animals. An optimized set of high efficiency filters (10 narrow band (30nm) excitation,18 narrow band (20nm) emission filters) and advanced spectral unmixing algorithms allow spectral scanning over blue to near infrared wavelengths with visualization of multiple reporters (bioluminescent and/or fluorescent) in the same animal. 3D diffuse tomography for both bioluminescent and fluorescent optical signals can be quantified to determine source location, and concentration, and analyzed to provide anatomical context following co-registration with the digital mouse atlas (or other imaging modalities e.g. µCT, or MRI). Training with mouse (XPM-2 bioluminescence, and XFM-2 fluorescence) phantoms provide users with experience acquiring images under various settings for analysis with Living Image Software. Entry to the IVIS Imaging Facility is by authorized card access only. The IVIS Spectrum has applications in many fields of research – such as oncology, stem cell research, infectious disease, toxicology, gene therapy, neurology, drug metabolism, immunology, and transplant biology.