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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.

 

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 Promethion and GridION instruments are available for long-read sequencing. 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. 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 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 2400 sq. ft. of laboratory space in the basement of the Biochemistry Building (Rooms 7, 11, and 13). 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, scheduled within safe social distancing guidelines for the building, and hourly or per-sample fees are charged based on the instrument. The facility houses three GC/MS instruments (Agilent 5975 and Thermo DS-Q single quadrupole systems and a Waters GCT Premier GC-TOF system), one triple quadrupole GC/MS/MS instrument (Agilent 7010B equipped with CTC PAL autosampler capabilities for headspace analysis and a Chromtech TDAS 2000 system for thermal desorption analysis), four triple quadrupole LC/MS/MS systems (Waters Xevo TQ-XS, Xevo TQ-S micro, Xevo TQ-S, and Acquity TQ-D), one Thermo Q-Exactive LC/MS/MS, two Waters Xevo G2-XS QTof LC/MS/MS systems, and a Shimadzu cfr-plus MALDI-TOF mass spectrometer. 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 CompoundDiscoverer software, and Agilent Profiler and MassProfiler Professional (MPP) software is used for untargeted analysis of GC/MS data. Data files are archived nightly to a 50 TB RAID 6 NAS archive.

 

Proteomics Core

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 1000 UPLC and a Thermo Scientific Q-Exactive HF-X interfaced with a Thermo Scientific EASY nLC1200 UPLC, both with Flex-Spray Ionization Sources. Together these systems combine 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 them ideal for deep proteome profiling of complex samples and highly specific peptide quantitation. 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 Q+S for data visualization, statistical validation, and testing. Up-front chromatographic fractionation of complex peptide samples is offered using a Waters Acquity H-class UPLC for deeper MUDPIT-style analyses.

 

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 RTSF IVIS Spectrum Core at Michigan State University is a versatile, advanced in vivo bioluminescent and fluorescent pre-clinical imaging system that combines high-throughput and full tomographic optical imaging in one platform. The IVIS Spectrum Imaging System allows non-invasive, sequentially In vivo imaging over time yielding valuable information on disease progression, cell trafficking and gene expression patterns in living animals. The IVIS Spectrum with integrated gas (isoflurane) anesthesia, 5-position manifold and heated stage allows for high throughput (up to 5 mice at a time) quantitative bioluminescent and fluorescent imaging in vivo in a light tight imaging chamber. The Imaging Wizard guides the user through imaging set-up and acquisition. Narrow band excitation and emission filters and spectral unmixing algorithms allow spectral scanning over blue to near infrared wavelengths. Multispectral imaging and advanced spectral unmixing algorithms allow visualization of multiple reporters (bioluminescent and/or fluorescent) in the same animal. Living Image software allows 3D reconstruction and quantitation of optical signals for both bioluminescent and fluorescent sources while co-registration with the digital “mouse atlas” (or other imaging modalities) provides anatomical context of reconstructed optical data. An adjoining room (286 sq. ft.) provides animals housing, a 6ft. NuAire class II type A2 biosafety cabinet, and benchtop anesthesia machine for animal manipulations/procedures.

 

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