DaCCoTA Cross-Institutional Scientific & Translational Resource Guide
The DaCCoTA Cross-Institutional Scientific & Translational Resource Guide provides a list of the research equipment available at partnering DaCCoTa institutions. This document is updated annually or upon submission of new information by institutions. If you find inaccurate information, please email firstname.lastname@example.org.
UND Core Facilities
The ND INBRE Informatics Core is undergoing a restructuring due to the relocation of the Director and new initiatives requiring informatic expertise in health disparities and clinical translational research. Recruitment for the Informatics Core will focus on complimenting two new areas of focus at the UND SMHS. The first is to strengthen the collaboration between the INBRE and the newly funded Dakota Community Collaborative on Translational Activity (DaCCoTA). This five year, $20,000,000 award comprises a partnership among entities in ND and SD to stimulate translational and clinical research. The award includes a core dedicated to community engagement research with a prominent focus on the health disparities within the American Indian population. This new NIH CTR award provides the ND INBRE with the opportunity to develop a new focus of collaboration with researchers across both ND and SD and to leverage resources between the awards. The ND INBRE can provide expertise in bioinformatics and medical informatics and gain expertise for the INBRE partners in biostatistics, epidemiology and research design; a strength of the DaCCoTA. The search committee is in place and the first solicitation was filed in March of 2019. In addition, the ND INBRE will continue to serve the TCU and PUI partners with expertise in biostatistics, bioinformatics and medical informatics.
The Human Tissue Repository Core (HTRC) facilitates storage and dispersal of human tissue samples. These samples will be available for all researchers across campus, such as researchers in the Host-Pathogen Interaction COBRE (Center of Biomedical Research Excellence). The core resides in the Department of Biomedical Sciences at the UND School of Medicine & Health Sciences. The HTRC provides various well-conserved, formalin-fixed human tissue samples for scientific research to enhance translational relevance. We may also provide simple demographic and histopathologic information about these samples to correlate with clinical data while maintaining confidentiality for these patients. The HTRC helps guide your preparation of IRB protocols, procure and store tissue specimens (e.g., nasal and respiratory tissues, etc.). The HTRC also provides some technical assistance to perform human-subject-related research and promote collaborations. The Core is directed by Dr. Min Wu (email@example.com).
The INBRE Microscopy Core (IMC) is a new core facility. Established and maintained by the North Dakota INBRE program, this core is located in room W471 in the UND School of Medicine & Health Sciences building. The mission of the IMC is to enhance research productivity, research funding and STEM efforts for the partners of North Dakota INBRE by providing instrumentation, expertise and training in microscopy. The equipment is available to all UND investigators as well as all off-campus investigators. The core is equipped for the microscopic examination of cells and tissues and includes the following instrumentation: a Leica LMD6 Laser Microdissection Microscope System, a Leica Personal Confocal TCS SPE Microscope, an Olympus BX63 Upright Fluorescence Microscope, and an Olympus FV3000 Laser Scanning Confocal Microscope with Live Cell Imaging capabilities. The facility is under the direction of Dr. Van Doze (firstname.lastname@example.org) with assistance from Dr. Swojani Shrestha (email@example.com), a postdoctoral research fellow, who assists with its daily operations.
The ND-FCCS Core is a joint effort between the departments of Biomedical Sciences and Pathology at the UND School of Medicine & Health Sciences and the North Dakota INBRE (P20GM103442) and the Host Pathogen COBRE (P20GM113123). The ND-FCCS Core maintains both a BD Symphony flow cytometer with 4 lasers and >30 color high throughput cell analysis and a BD FACSAria II flow cytometer with 3 lasers allowing for 4-way first pass sorting with up to 9 colors. The ND-FCCS Core also supports both FACSDiva analysis software and an institutional FlowJo license. The core staff consisting of Dr. Bradley (Core Director), Dr. Knopick (Core Asst. Director), and Steven Atkins (Core Technical Advisor) provide training on the instrumentation and software as well as consultation for experimental design and data analysis. Cell analysis is available on the BD Symphony by trained investigators or on a for-fee basis by core staff. Cell sorting is available as a full-service product of the ND-FCCS Core. The facility is directed by Dr. David Bradley (firstname.lastname@example.org).
The Genomics Core (a combined genomics and bioinformatics core) at the University of North Dakota is a shared resource providing state-of-the-art genomics resources to investigators at UND, institutions across the northern Midwest, as well as external commercial clients. The core facility is a COBRE-funded operation intended to help regional researchers utilize next generation sequencing technologies in basic and translational genomic research. The core provides services, training and genomics resources to the scientific research community here at UND, NDSU, USDA and nearby colleges. Core staff are available to design, analyze and visualize sequencing data based on needs of individual investigators and research projects. The Genomics Core group provides services in data analysis using standard analysis pipelines as well as project-specific analysis, both of which are free of charge. The Core’s primary function is to help researchers generate genomics data, analyze, interpret, visualize and store the massive amount of data produced in next generation sequencing experiments.
The Genomics Core has a well-equipped lab for various types of library preparation and to support the sequencing needs of investigators. The core provides Poly-A-selected and Ribo-depleted (directional or non-directional) library preparation services for RNA-Sequencing. The Genomics Core also prepares DNA libraries for whole genome sequencing based on requests from various research groups. The core recently started library preparation service for long read platform using the VolTrax system. The Genomics Core staff train and help investigators in library preparation for ChIP-Seq, ATAC-Seq, microbiome and bisulphite sequencing. The Core also supports analysis of these investigator-made specialty libraries. The Core lab is equipped with an Illumina MiSeq short-read sequencer and a Nanopore GridION X5 long-read sequencing platform along with a variety of instrumentation to support sequencing and QC needs for NGS-based experiments. The Genomics Core facility is equipped with a 10X chromium system (10X genomics) for single-cell genomics, which is capable of doing transcriptomics, ATAC-Seq and DNA sequencing at single cell level.
The Genomics Core has two high performance workstations, Buddy and Bart, for data analysis. Each of these servers is equipped with Intel Xeon E5-2687W v2 processors (8 HT Cores, 3.4GHz), 256 GB 1866MHz DDR3 RAM, a NVIDIA Tesla K20c GPU, and 24 TB of storage space. Data is backed up in raid5 configuration. Additional data is backed up in tapes at the University of Oklahoma. Data is stored on a 50 TB shared network drive administered jointly by the Core and UND IT. Data collected by the Core and UND investigators is stored redundantly on a Dell SC4020. The Core is directed by Dr. Bony De Kumar (bony.dekumar@UND.edu).
The Imaging Core Facility at the UND School of Medicine & Health Sciences provides advanced instrumentation for clinical and basic science researchers interested in investigating biological and disease processes at the tissue, cellular, sub-cellular and molecular level. Equipment includes a Leica Stellaris confocal, an Olympus FV1000MPE multiphoton/single photon microscope system for intravital imaging, an Olympus IX83 TIRF microscope system, a Leica Thunder fluorescent microscope, a Nikon Eclipse80i fluorescent microscope, a Hitachi 7500 TEM, a Hitachi 4700 field emission SEM, and equipment for preparation of samples for light and electron microscopy. The facility also houses a workstation computer equipped with state-of-the-art image analysis software. A wide range of services and applications are supported by the Imaging Core including fluorescence and brightfield microscopic imaging and analysis of fixed tissues and tissue arrays, live cell and tissue imaging, 3D imaging, fluorescence imaging assays, TIRF microscopy, thin section TEM, and SEM. The core is directed by Dr. Bryon Grove (bryon.grove@UND.edu). Please visit the core website for detailed information on all machinery and services available.
The Mass Spectrometry Core facility was established by the COBRE (Center of Biomedical Research Excellence) program in Pathophysiology of Neurodegenerative Diseases, NIH National Institute of General Medical Sciences, grant number P30GM103329. The facility provides instrumentation, expertise, and training in mass spectrometry to all campus investigators as well as off-campus investigators. The Core is equipped with five state-of-the-art LC-MS/MS and GC-MS/MS instruments including high-resolution accurate mass analyzers. The main focus of the Core is on targeted and untargeted metabolomics including lipidomics, pharmacokinetics, small molecule identification and structure validation, targeted and untargeted proteomics, and metabolome and proteome comparison between experimental groups. The facility is directed by Dr. Mikhail Golovko (email@example.com).
The Behavioral Research Core Facility (BRCF) is part of the Center for Biomedical Research located within Columbia Hall. The mission of the BRCF is to enhance productivity and collaborative efforts of IDeA-state investigators by offering a variety of state-of-the-art tools to assess motor, sensory, and/or cognitive behavior in rodent models of human diseases. The BRCF is jointly managed by the ND INBRE and the Department of Pathology at the UND School of Medicine & Health Sciences under the direction of Dr. Van Doze (firstname.lastname@example.org).
The Histology Core, located within suite W162 of the UND SMHS, provides investigators with cryostat and microtome equipment access and the necessary technical expertise to prepare samples for a wide variety of high-resolution imaging techniques. For users wishing to access the equipment, the Core technical staff provides training and assistance with tissue fixation protocols, paraffin and frozen sectioning, a variety of special stains, and immunohistochemistry. The Core also maintains a service-oriented operation allowing users to deposit tissue samples and request embedding, specific sectioning, and staining procedures. The Core is directed by Dr. Colin Combs (email@example.com).
North Dakota State University (NDSU) Facilities
This Molecular Biology Lab has multiple units including a tissue culture room, a bioassay section, and a bacterial cell culture room, which houses the necessary equipment to do biochemical, cellular, and molecular biology research. The Molecular Biology Lab contains Applied Biosystems 7500 Fast Real-Time PCR systems; a BD FACS Jazz cell sorter; an Accuri C6 Flow Cytometer; an Agilent 2100 Bioanalyzer; a Biotek H1MF microplate reader; a Storm 865 imager with ImageQuant TL software; a Thermo Scientific NanoDrop 2000C; a Gemini EM Fluorimeter; Applied Biosystems Thermo Cyclers; a GenePix 4000B Microarray Scanner; Eppendorf 5430, 5417R, and 5418 Centrifuges; a Beckman Allegra 25R Centrifuge; polyacrylamide gel electrophoresis rigs and trans blot; and agarose gel electrophoresis boxes . The tissue culture room contains 3 tissue culture hoods, 3 incubators, a Nexcelom cell counter, a fluorescence inverted microscope and various light microscopes, a Beckman Allegra X-12R centrifuge, and Cryo-Safe liquid nitrogen cell storage. The bacterial cell culture room contains a cell culture hood, a shaker, a BTX electroporation system, and a Beckman Microfuge 18 centrifuge. In addition to equipment, the Core Biology Facility is able to provide reagents and consumables, consultation, and support staff to aid in research. This core is directed by Dr. Tao Wang (firstname.lastname@example.org). Visit its website for more information about pricing. DaCCoTA awardees with NDSU collaborations will receive the internal rate. Other DaCCoTA awardees will incur a 45 percent surcharge.
The Advanced Imaging and Microscopy Core Facility has the following resources available:
- Zeiss Axio Observer Z1, fully motorized inverted scope with LSM700 laser scanning head attachment with possibility to use FRET, FRAP, and TIRF; advanced epifluorescence; ApoTome attachment for structured illumination 3D imaging; DIC and PlasDIC set; Definite Focus; heated stage; environmental control chamber (O2, CO2, and humidity) for time-lapse cell culture related experiments with Zeiss Axio Cam MRc Rev3 black and white, and Zeiss HRc Rev3 color camera; and Zeiss Zen Black along with Zeiss AxioVision Rev. 4.8.1 microscope control and image analysis software
- Zeiss Axio Imager M2 fully motorized upright microscope with advanced epifluorescence (Colibri2), ApoTome2 attachment for structured illumination, 3D imaging, DIC, Zeiss AxioCam MRm Rev3 black and white and Zeiss AxioCam HRc Rev3 color cameras, AxioVision Rev 4.8.1 microscope, and image analysis software
- Zeiss Lumar, V12 stereo motorized microscope, fluorescence and bright field, with Zeiss AxioCam HRc. Rev3 color camera, Photometrics CoolSnap ES black and white high resolution camera equipped with NeoLumar S 0.8x WD=80mm and NeoLumar S 1.5x WD=80mm long working distance lenses, heated stage as well as Zeiss AxioVision Rev. 4.8.1 microscope control and image analysis software
- Zeiss Laser Microdissection and Pressure Catapulting System; Zeiss Axio Observer Z1 fully motorized inverted scope platform with PALM MicroBeam IV System with AxioCam ICc R4 and Zeiss AvioCam Hrc Rev3 color cameras for Brightfield and Photometrics CoolSnap CF black and white camera; advanced fluorescence, PlasDIC set, RoboSoftware Pro and Zeiss AxioVision Rev.4.8.1 image capture, system control and image analysis software.
This core is directed by Dr. Pawel Borowicz (email@example.com), and the fee structure is provided on its website. DaCCoTA awardees with NDSU collaborations will receive the internal rate. Other DaCCoTA awardees will incur a 45 percent surcharge.
The Histology/Pathology units have the following equipment available: Leica RM2255 Microtome, Leica Cryostat, Leica Tissue-Tek TEC 5 Embedding System, Leica ASP300 S Automated Tissue Processor, Paraffin Trimmer, antigen retrieval pressure system, slide staining stations, and slide dryers.
This core is directed by Dr. Pawel Borowicz (firstname.lastname@example.org), and the fee structure is provided on their website. DaCCoTA awardees with NDSU collaborations will receive the internal rate. Other DaCCoTA awardees will incur a 45% surcharge.
This is a central multi-user imaging facility serving more than 100 researchers annually, including faculty and students across 20 NDSU departments and five colleges as well as industrial users. The Electron Microscopy Center houses nearly $5 million worth of advanced technical equipment including the following: A) a confocal scanning light microscope, B) bright field and dark field light microscopes, and C) complete image-handling capability with major instrumentation consisting of two transmission electron microscopes (TEM), two scanning electron microscopes (SEM) with energy dispersive x-ray capability, and a micro computed tomography system (micro CT). The core is directed by Dr. Scott Payne (email@example.com, firstname.lastname@example.org). The fee structure is provided on their website. DaCCoTA awardees will receive the internal rate. Additional charges may be incurred for labor time based on the project/work.
NDSU Animal Studies Core Facility
The recently renovated (COBRE-supported) Animal Studies Core Facility is part of the
Department of Pharmaceutical Sciences at NDSU. This facility has 5 individual rooms
(70 square feet each) controlled by KJS Intelligent Environment Control Systems (temperature,
humidity, light control). Pathogen-free Innovive IVC System (Innovive, San Diego,
CA) and Biosafety level 2 cabinets are located in the animal facility for nude mice
experiments. A Leica CM1950 cryostat and a VisualSonics Vevo 3100 ultrasound imaging
instrument (25 and 55 MHz transducers) are located in a room adjacent to the animal
facility for cryosectioning. There is also an animal surgery room (207A2) for performing
surgery and anesthetizing and euthanizing the animals. Two full-time technicians
with expertise in orthotopic mouse models of different cancers (pancreatic, prostate,
breast, colorectal, etc.) are available for protocol development, study design, training
of students and postdoctoral researchers, execution of the projects, etc. The core
is directed by Dr. Jodie Haring (Jodie.Haring@ndsu.edu), and Megan Ruch (Megan.C.Ruch@ndsu.edu) is the Animal Facility Technician.
DaCCoTA awardees will receive the internal rate. The per diem rate of .95/day includes bedding, food, water, cage washing, room space, IVC racks, and consumables. Visit their website to view other service charges.
The Pharmaceutical Sciences Department has recently purchased a high-resolution ultrasound imaging instrument (VisualSonics Vevo 3100) with 25 and 55 MHz transducers for imaging orthotopic tumors in small animals. Contact Dr. Sanku Mallik (email@example.com) for more information. In addition, the Health, Nutrition, and Exercise Science Department on the NDSU campus has a medical ultrasound imaging instrument (Terason t3200 with numerous transducers covering the frequency range 2 – 26 MHz). Contact Dr. Kara Gange (firstname.lastname@example.org) for availability.
PIs will have access to the following instruments through the Office of Research and Creative Activity at NDSU:
Series 1100 High-Performance Liquid Chromatography: The Agilent 1100 Series HPLC consists of a diode-array detector (DAD), fluorescence detector (FLD), fraction collector, quaternary pump, autosampler, thermostatted column compartment and vacuum degasser.
Raman Spectroscopy: PIs will have full access to a Nicolet NXR 9650 FT-Raman spectrometer, which is capable of producing high-quality Raman measurements using high-speed scanning, sample mapping, screening applications, and kinetic analysis. The spectrophotometer can measure organic and inorganic samples using a spectral range down to 100 cm-1.
Symyx® Batch Synthesis Station: The Symyx® batch reactor system gives PIs full capacity to do multiple polymer synthetic reactions in a multiplexed pattern using a synthetic batch station, which is equipped with a dual-arm liquid dispensing robot that is housed inside a glove box under dry nitrogen. The inert environment allows for open containers of sensitive reagents to be located on the deck for aspiration and dispensing into the array vials. Liquid viscosities up to 50 cps can be accurately dispensed.
NDSU Center for Nanoscale Science and Engineering: The NDSU Center for Nanoscale Science and Engineering, which is part of the Research Operative Services Center, has the following equipment available: FTIR spectrometers for composition analysis; a TA Instruments Q1000 differential scanning calorimeter for thermal analysis of polymer samples; a TA Instruments Q800 DMA for viscoelastic analysis of polymer films; a Waters Gel Permeation Chromatography system for molecular weight determination of polymers; a Symyx Parallel Batch Polymerization System for synthesis of polymers in an array format; a Chemspeed Autoplant A100 Polymerization system for synthesis of polymers in automated parallel reactor vessels; a Symyx Parallel Coating/Polymer Formulation System for preparation of polymer solutions and viscosity measurement; a Symyx Coating/Polymer Film Application System for preparing films of polymers for analysis; a Symys Rapid GPC for molecular weight analysis of polymers; a Bruker Vertex 70/HTS FTIR System for compositional analysis of libraries of polymers; a Symyx Surface Energy system to measure the surface energy of polymer films; a Symyx parallel DMTA system to determine the viscoelastic properties of up to 96 polymer samples simultaneously; an Agilent GC-MS for analysis of chemical samples; an Agilent HPLCMS system for separation and analysis of reaction products; a Synergy HT microtiter plate reader for analysis of fluorescence in various assays; and a Bruker Ultraflex MALDI-TOF for the mass spectral analysis of polymers.
Aaron Reinholz (email@example.com) is the Director of Research Operations. Visit the recharge center for more information. DaCCoTA awardees will receive the internal rate, and additional charges may be incurred for labor time based on the project/work.
The Department of Pharmaceutical Sciences has the following equipment: A) Olympus Laser Microscope with shutter control system for live imaging, B) Beckman model 5500B gamma counter, C) IR and visible spectrophotometer, D) LC/MS system (Agilent), E) Leica DMi8 fluorescence microscope, F) CEM Microwave Protein Synthesizer, G) Electron paramagnetic resonance (EPR) spectroscopy, H) LABCONCO Freeze Dryer, I) High speed centrifuge (Beckman) and Ultracentrifuge (Beckman), J) Vevo 3100 micro-ultrasound preclinical imaging system, K) Electroporator (CUY21 EDIT Version, NEPA Gene Co), L) VirTis Homogenizer, M) CO2 incubator, N) Beckman GPR centrifuge, O) Twelve diffusion cells modified for iontophoresis (Franz type) with drive console to accommodate all the cells, P) Twelve Franz type diffusion cells with two drive consoles each accommodating 6 cells, Q) SceptorR iontophoretic programmable power supply that allows six diffusion cells to be run simultaneously and provides multichannel AC or DC prescription set, R) TewameterR for TEWL measurements, S) CorneometerR for skin capacitance measurement, T) IR Thermometer, U) Three Hewlett Packard HPLC systems and LC-10AD Shimadzu Liquid Chromatograph, V) Hewlett Packard 5880A Series Gas Chromatograph, W) FT-IR (Nicolet 208), X) VP-DSC (MicroCal), Y) SpectroMax M5 (Molecular Devices), Z) Bio-Rad Mini –Protean Tetra systems, AA) Common use Tri-Carb 2100 TR liquid scintillation counter, AB) Jasco J-815 Circular Dichroism Spectrometer, and AC) ZOE Fluorescent Cell Imager.
The Department of Chemistry and Biochemistry has Varian 300, 400, and 500 MHz NMR instruments available. The 500 MHz instrument has a triple axis gradient capability. The NMR facility was renovated in 2014 and has one full-time staff member to train the users, help them set up their experiments, and assist with data interpretation.
Coating and Polymeric Materials Equipment Facility
The Department of Coatings and Polymeric Materials has a Thermo Scientific Nicolet 8700 Fourier Transform Infrared Spectrophotometer, a Varian Cary 5000 Ultraviolet-Visible-Near Infrared Spectrophotometer, a Jobin Yvon Horiba Fluoromax-3 Fluorescence Spectrophotometer, electrochemical impedance spectroscopy, atomic force microscopy (Veeco DI-3100 AFM), and a scanning probe microscope (Veeco Nanoscope IIIa MultiMode SPM) as well as a dynamic light scattering (Nicomp 380), single particle optical sizing (Particle sizing systems SPOS 780), and zeta potential analyzer (Agilent Technologies, Colloidal Dynamics AcoustoSizer IIs). This facility also provides access to Gel Permeation Chromatography (GPC) from the Waters Corporation, which uses THF as the mobile phase. This is a modular system with Refractive Index and UV detector for molecular weight characterization of macromolecules.
DaCCoTA investigators using the prime core facilities will be charged at the internal rate of NDSU. Visit the Research Operations Recharge Center for more information. Other facilities may incur additional charges. Please contact the core directors for further information. To use specific departmental facilities at NDSU, please contact appropriate department chair. The fees structure may vary based on project and utilization.
University of South Dakota (USD) Facilities
This core provides dedicated staff and has following equipment:
- The Vevo 2100 Ultrasonography System (VisualSonics) is equipped to non-invasively evaluate tumors in both 2D and 3D. This technology allows researchers to monitor key biological parameters such as the volume of tumors in 3D as well as their perfusion and vascularization status in live animals. Because of the non-invasive nature of ultrasound, tumor progression and vascularization can be longitudinally monitored and quantified by high-resolution ultrasound imaging in rodent models of cancer. The capabilities and accuracy of this ultrasound imaging system were illustrated in a research article published in 2016 (Freeling and Rezvani, 2016).
- The MousePOD and LI-COR fluorescent imager (LI-COR Biosciences) are powerful tools for assessing tumor growth and its behavior in live animals. This technology allows antibody-targeted labeling of tumors by tail-vein injection followed by scanning of the whole animal. This technology will allow repeated evaluations of the total tumor burden at the primary and metastatic sites in rodent models of cancer. An example can be found in a research article published in 2015 (Abdullah et al., 2015).
- The S6 D Stereomicroscope equipped with an EC3 digital camera (Leica) and associated analysis software will enable the capturing of images of tissues at necropsy. The software will enable highly accurate quantification of tumor dimension and area.
- A fully equipped surgical and necropsy station including surgical instrumentation, anesthesia induction, and animal monitoring. Knowledgeable staff are available for training or performance of techniques including the xenograft and orthotopic tumor transplantation models.
Rates and Policies:
|User Charge||FY20 Approved Rate|
|Analysis Services - Internal/Fed Funded External||$132.00|
|Multi-Use Services - Internal/Fed Funded External||$60.00|
|Surgery Services - Internal/Fed Funded External||$87.00|
|Ultrasound (ECHO) Services - Internal/Fed Funded External||$121.00|
This core's new confocal imaging system is a SP8 confocal on a DMi8 microscope from Leica. It is outfitted with CO2 and incubation systems for live cell imaging. It has a second “Resonant scanner” for high speed image acquisition (40 fps @ 512x512 nm). It employs only two excitation lasers, a 405 nm diode laser and a tunable “White light laser” that is tunable for any excitation wavelength between 450-650 nm. This core also has a “Spectral detector”, which allows the investigator to choose the emission wavelengths they wish to measure. Additionally, this avoids cross-talk and bleed-through fluorescence from other channels. The system is also outfitted to do two types of super resolution imaging, aka nanoscopy. Traditional confocal image resolution could only reach a 200 nm resolution. The LAS-X analysis software allows users to use a smaller pinhole in combination with deconvolution analyses to capture images between 120-150 nm. Additionally, the system also includes a 3X STED, wherein we can do up to 3 color STED images using a 775 STED depletion laser to image structures below 50 nm easily and down to 10-20 nm with empirical optimization. The core’s confocal imaging system is set up to perform FRAP, FRET, photo-activation, or photo-conversion experiments. The LAS-X software also includes FRET wizard and FRET quantification applications. For more on doing FRET on our system please see the website below: http://bbic.nsm.uh.edu/protocols/fret-leica-sp8
Rates and Policies
Unassisted Imaging — Peak Hours
Unassisted Imaging — Off-peak Hours
|Leica SP8 confocal||$60/hour||$30/hour||$15/hour|
This core has an Axon GenePix 4000b scanner (Molecular Devices, Sunnyvale, CA), an Applied Biosystems StepOnePlus real-time PCR, an Agilent Bioanalyzer, and the Amaxa nucleofection system. This core’s support ranges from training on how to work, isolate, and study RNA and DNA to running and analyzing DNA microarray experiments. This core provides real time RT-PCR and the TaqMan proximity ligation protein assay with real-time PCR for protein-protein interaction study.
Rates and Policies
Contact Genomics Core Director Kathleen Eyster (firstname.lastname@example.org) for a quote or for details about available services.
The Proteomics Core provides the researcher with access to a LiCor Odyssey (LiCor Biosciences, Lincoln, NE), an Amersham Typhoon 9410 Imager (GE Healthcare Bio-Sciences Corp., Piscataway, NJ), a Bio-Rad VersaDoc 5000 Imaging System (Bio-Rad, Hercules, CA), a NanoAcquity UPLC coupled to a Waters Micromass electrospray quadrupole/time-of-flight hybrid high-resolution mass spectrometer (Q-ToF) (Waters, Milford, MA), and a ProteomeWorks Spot Cutter. This facility also offers software for quantitative proteomics analysis and post-translational modification (PTM) analysis.
Rates and Policies
|Charge Description||FY20 - Internal/Fed Funded External|
|Protein Analysis from band or spot – BBS Faculty||$107.00|
|Protein Analysis – Gel-free or Gel-LC***##||$543.00|
Note: the service includes:
-Consulting and advice in sample preparation and shipping
-Sample processing (includes pH adjustment, reduction and alkylation followed by trypsin digestion)
-Shotgun proteomics analysis that includes nanoUHPLC fractionation and tandem -mass spectrometry analysis (MS/MS analysis)
-Bioinformatics analysis: Mascot, Proteome Discover, and GPM servers for protein identification and characterization, the ProteoIQ program for data organization and relative quantification, as well as other tools.
-Assistance in data analysis, organization, visualization, and interpretation
This core is managed by Dr. Eduardo Callegari (Eduardo.Callegari@usd.edu)
This core has a new BD Accuri C6 plus flow cytometer as well as a new generation of BD cell sorter called Melody. An experienced technician provides investigators with a resource for analytical studies using flow cytometry.
Rates and Policies
|Service Instrument/Item||Internal/Fed Funded External|
|BD Accuri C6 plus||$22/hour|
|BD cell sorter called-Melody||$39/hour|
This core provides services for the preparation of histology and immunohistology slides. Available equipment includes tissue sectioning cryostats, microtomes, and paraffin-embedding ovens. Various stains such as Hematoxylin and Eosin and immunohistological techniques including fluorescent-antibody labeling are available. The equipment in this core is available for use by researchers themselves, or slide/tissue preparation services may be requested.
Rates and Policies
Contact Dr. Khosrow Rezvani (email@example.com) for a quote or for details about available services.
Each Behavioral Core testing room has overhead cameras connected to computers with automatic tracking systems (EthoVision XT; Noldus Information Technologies) and observer-based event recorder behavioral software (Observer XT; Noldus Information Technologies). The behavioral equipment available for use includes infrared elevated plus mazes, a radial arm maze, water mazes, open fields, forced swim tests, rotarods, T-mazes, foot-shock boxes, and conditioned place preferences. The core also supplies a portable camera, computer, and mPEG encoding units so that investigators can record behavioral footage outside the core facilities (i.e., in the Biology Dept). These computers also have Observer XT loaded on them.
Rates and Policies
The current FY20 charges for internal users are $2855/project. This includes use of the equipment, rooms, cameras/software, and training for the researchers.
Contact Jamie Scholl (Jamie.Scholl@usd.edu) for a quote or for details about available services.
All seven of the above cores facilities will be available to DaCCoTA investigators at the same rates as USD faculty.
Facilities at Sanford
The primary goal of the Animal Behavior Core is to provide expertise on a number of animal behavior tests, including assays for learning and memory, spatial navigation, visual processing and acuity, and motor performance. The core staff can provide education and training on how to set up and analyze various behavioral tests, comprehensive data collection, data analysis, and data interpretation. This core is managed by Katherine White (Katherine.White@sanfordhealth.org).
The goal of the Analyte Core is to provide quality biologicals and assay development to the investigators. Services provided by the core include design, production, and purification of proteins to be used in pre-clinical therapeutic and assay development. The core also has the capabilities to design and test assays. This core is managed by Rick Evans (Rick.Evans@sanfordhealth.org).
The Sanford Health BioBank was established in 2011 to advance Edith Sanford Breast Cancer Research and support ongoing research programs in a broad range of health conditions. Sample processing is performed in a state-of-the-art laboratory dedicated to the processing and handling of biospecimens for research purposes. The laboratory is equipped with custom liquid handling instruments and high-throughput automated DNA extraction instruments to facilitate the processing of samples. Samples have been collected from thousands of patients and are stored in the Biobank for future research. This core is managed by Linda Berg (Linda.Berg@sanfordhealth.org).
CoRDS is a central patient registry for all rare diseases designed to collect contact and clinical data on rare diseases and to provide a mechanism to connect patients interested in participating in research with the researchers who are conducting the studies or clinical trials on rare diseases. Coordinating a patient registry for multiple, and potentially all, rare diseases offers potential to patients and their families, patient advocacy groups, and researchers studying rare diseases. This core is managed by Benjamin Forred (Benjamin.Forred@sanfordhealth.org).
The mission of the Flow Cytometry (FCM) Core is to provide high quality, efficient and affordable analytical and preparative flow cytometry resources to investigators including physician scientists in order to serve both basic science and translational research. The FCM Core currently holds 4 cytometry instruments and 1 sorter: 2 Accuri C6 flow cytometers with 2-lasers and 4-detectors, a bench top-type Guava EasyCyte HT flow cytometer with 2-lasers and 6-detectors, BD FACS LSRFortessa SORP with 5 lasers and 21 colors, and a BD FACSJazz sorter with 3 lasers and 6 colors. The FCM provides the following services: a) Cellular sorting service by flow cytometry, including pre-enrichment of cell populations by magnetic beads-based cell isolation; b) Assistance in cell sorting assays; c) Assistance for analytical flow cytometry experiments using core instruments; d) Flow cytometry consultation: training, education on applications including sample preparation methods, designing FCM experiments, assessing project feasibility, interpretation of the data, and preparation of methods for manuscripts. This core provides full-time employees responsible for service/maintenance of all equipment and assistance in personnel training and data collection. This core is directed by Alexei Savinov, MD, PhD (Alexei.Savinov@sanfordhealth.org).
The goal of the Imaging Core is to provide light, fluorescence, and confocal microscopy to visualize both living and fixed cells. We are equipped with three confocal microscopes (Nikon A1R with resonant scanner, Nikon A1 with TIRF capabilities, and Olympus FV1000) with capabilities for 4-color simultaneous imaging and spectral imaging, a Leica Aperio VERSA combination Brightfield and fluorescence slide scanner, the Cell Insight CX7 High-Content Screening Platform with spinning disk confocal capabilities, a MicroBrightfield Stereo Investigator image analysis microscope and workstation, a MetaMorph basic offline image analysis software package, and multiple upright and inverted light and fluorescent microscopes. Core personnel will provide training in equipment use and assist in the development of routine and customized protocols in areas such as immunofluorescent staining, live imaging, tagged fluorescent protein visualization, FRET, FRAP and TIRF analyses, and 3-dimensional image reconstruction. This core is directed by Indra Chandrasekar, PhD (Indra.Chandrasekar@sanfordhealth.org) and Jacob Cain, Ph.D (Jacob.Cain@sanfordhealth.org).
The goal of the core is to provide quality services and training in molecular biology and genetics assays, including nucleic acid extraction and quality analysis, quantitative real-time PCR analysis, RNA in situ hybridization, CRISPR/Cas9-mediated genome editing, and chromatin immunoprecipitation for sequencing/qPCR. Additionally, the core serves as an interface between investigators at Sanford Research and the Functional Genomics Core and DNA Analysis Core at the Sanford Prebys Burnham Medical Discovery Institute (SPB) to provide high-throughput sequencing. The Functional Genomics and Bioinformatics Core will also provide assistance with experimental design, resource assessment, sample preparation, assay performance, and data analysis and management. The core will also provide bioinformatics support for analysis of RNA-seq and ChIP-seq results. Core personnel will provide detailed and customized protocols of the methods for manuscript or grant preparation. This core is led by Kameswaran Surendran, PhD (Kameswaran.Surendran@sanfordhealth.org) with assistance from Mike Kareta PhD (Michael.Kareta@sanfordhealth.org).
The primary role of the Molecular Pathology Core (MPC) is to provide histology support and expertise in pathology. The major services provided by the MPC are processing and embedding tissues, sectioning of paraffin-embedded and frozen tissues, and staining of tissue sections. The MPC offers routine hematoxylin/eosin staining of tissue sections. The core has extensive expertise in antibody optimization and performing immunohistochemical staining, including colorimetric double staining. Specialty stains are performed as needed, including PAS, Oil Red O, Masson’s trichrome, and phalloidin stain. The core also has the ability to create custom tissue microarrays. To provide a comprehensive approach to cancer pathophysiology, the MPC offers assistance with live, small animal imaging, including fluorescent, luminescent, X-ray, and high frequency ultrasound modalities. This core is managed by Claire Evans (Claire.Evans@sanfordhealth.org).
The primary goal of the Biochemistry Core is to uniquely provide services for BioID, a method to screen for candidate protein-protein interactions based on proximity-dependent biotinylation. The core also provides a centralized resource of expertise, equipment, and technical capabilities that cover a variety of methods in the separation and analysis of complex biological samples. In addition, the core will coordinate the use of mass spectrometry services. This core is directed by Peter Vitiello, PhD (Peter.Vitiello@sanfordhealth.org) and Kyle Roux, PhD (Kyle.Roux@sanfordhealth.org).
The Research Design and Biostatistics Core at Sanford Research provides project assistance from the design phase all the way through data presentation. The core works with investigators to plan and design their studies and consult on the best ways to analyze and interpret data. With a broad range of statistical expertise, core staff are capable of applying the most efficient techniques to address research questions using the datasets generated from both observational studies and experiments. The Research Design and Biostatistics Core is comprised of three biostatisticians, a data analyst, and a medical writing consultant.
The core’s biostatisticians have a wide range of experience in study design, sample size calculation, and statistical analysis. They have the capability to perform all basic statistical analyses as well as several specialized methods such as multi-level modeling, survival analysis, factor analysis, cluster analysis, and social network analysis. The biostatisticians also have the ability to communicate efficiently with researchers in recommending study design, refining hypotheses, and determining statistical models appropriate for the study. The data analyst is proficient at extracting data, assuring data integrity, and running analyses for the biostatisticians to interpret. The analyst also assists clinical trials with data monitoring and reporting. The medical writing consultant assists researchers with protocol and manuscript writing. This core is directed by directed by Valerie Bares, PhD (Valerie.Bares@sanfordhealth.org).
DaCCoTA Investigators can access these cores at the same rates as Sanford Health Investigators. Please contact the core directors for more information about the charges associated with these services.