Functional Genomics Core Facility
We facilitate interdisciplinary gene function research and training in viral, bacterial, plant and animal systems.
We provide researchers with:
- Access to expensive, cutting-edge technologies (i.e. instrumentation) for functional genomics research at a minimal cost.
- Training and support on the optimal uses of these technologies.
- An opportunity to assist with and influence future purchases of functional genomics-related equipment.
Location
The primary suite is located in the lower level (Room 047) of the Edgar S. McFadden Biostress Lab and consists of three laboratory rooms containing various equipment necessary for studying the functions of genes. Additional equipment is located within the Avera Health and Science Center (SAV 313).
How to obtain Functional Genomics Core Facility access
The Functional Genomics Core Facility is accessible 24/7 for registered users through keycard access. All SDSU faculty and students can become registered users.
In order to become a registered user, individuals must first set up an account through the . From that website, users can set up a new account or log in to their existing account. Users will need to provide:
- First and Last Name
- Indicate User Group (Lab)
Additional information that can be provided is phone numbers for contact info and ORCID (recommended for linking publication history to core usage). If a lab group does not already exist, it can be created.
Approximately one to two days after submitting this information, the core staff will approve the initial account generation. Users can then log in to PPMS using their SDSU single sign-on and request room access and training through the PPMS system. Any issues or questions regarding account generation can be directed to Jenna Parliament.
How to reserve and access equipment
To use any equipment in the Functional Genomics Core Facility, you must type your PPMS ID and password (this should be your standard SDSU login information) into the computer associated with the instrument.
Please Note
You will not be automatically logged out. To end usage tracking, you must log out of the computer (lower right).
Do not store data on the computers in the Functional Genomics Core Facility. Computers are shared across users and can crash. For best data practices, either map your lab network drive and save data directly or send your data via Dropbox or OneDrive. USB drives are not allowed on core instruments as they represent a data and computer risk.
The Functional Genomics Core Facility is primarily a user-run facility. As such, researchers are responsible for providing their own labor. Training is available upon request through the PPMS system. Additionally, equipment manuals for many pieces of equipment are available upon request or digitally through our PPMS website.
Instrument maintenance is supported through user fees and associated prices.
Instrument Reservations
You can use the equipment on a walk-in basis if no one is already using the instrument that you need. If you are using a SDSU campus computer, you can .
Please note that all reservations will be billed according to the total reserved time. This is to encourage users to accurately book their time and avoid blocking the usage of others.
Acknowledging Functional Genomics Core Facility use
Proper acknowledgement of the use of Functional Genomics Core Facility equipment helps the facility obtain financial and other support to continue to provide essential resources to support academic research on the SDSU campus. Use the following statement when acknowledging use of the Functional Genomics Core Facility on publications, posters and presentations.
“This material is based upon work conducted using the South Dakota State University Functional Genomics Core Facility (RRID:SCR_023786) supported in part by the National Science Foundation/EPSCoR Grant No. 0091948, the South Dakota Agricultural Experiment Station and by the state of South Dakota. Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award No. P20GM135008. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health."
Contributions of support staff beyond simple training may warrant additional acknowledgement, including potential authorship. Failure to appropriately acknowledge use of core resources may result in revocation of access. To easily track publications associated with core usage we highly recommend linking your ORCID# with your PPMS account.
User Fees
- Users must supply all supplies and reagents needed during the operation of these instruments.
- To calculate prices for nonuniversity users, add 44.5% to the university price for each instrument.
- Usage rates calculated per hour unless otherwise indicated. Billing is for actual usage time (or reservation time) based on PPMS login down to the minute. Rates are also displayed on the PPMS website
| Equipment | Location | Cost ($/hr.) |
|---|---|---|
| QuantStudio 6 Flex Real-Time PCR System | SNP 047 | $16/run |
| LI-COR Odyssey Fc Imaging System | SNP 047 | $13/hour |
| BioTek Synergy 2 Multidetection Microplate Reader | SNP 047 | $12/hour |
| Octet R8 Biolayer Interferometry | SNP 047 | $40/hour |
| NanoDrop ND-2000 Spectrophotometer | SNP 047 | $9/hour |
| Beckman OPTIMA 130K Ultracentrifuge with MLS-50, TLA120.2 and MLA-55 rotors | SNP 047 | $1.80/hour |
| Olympus BX53 Upright Microscope with camera | SNP 047 | $8.40/hour |
| Olympus IX70 Inverted Microscope with camera | SNP 047 | $8.40/hour |
| Olympus FluoView 1200 Confocal Microscope | SNP 047 | $21/hour |
| Olympus SZX16 epifluorescent stereo microscope with camera | SNP 047 | free |
| Leica LIAchroic Confocal Microscope | SAV 313 | $28/hour |
| Nikon Ti2 widefield fluorescence microscope | SAV 313 | $15/hour; see equipment for long-term imaging rates |
| Leica CM1850 UV Cryostat with Cryovac and CryoJane Systems | SNP 047 | No cost: user provides consumables |
A variety of equipment is available to support research, ranging from PCR amplification to microscopic imaging.
Contacts:
- Functional Genomics Core Facility coordinator Ryan Hanson
PCR Systems
QuantStudio6 Flex RT-PCR
QuantStudio6 Flex Real-Time PCR instrument with both 96- and 384-well formats available. Multiplex capabilities including FAM, NED, ROX, SYBR and VIC. Touchscreen and software based setup and data export.
Potential applications:
- Analysis of gene expression through both single and multiplex assays
- Absolute quantifications with standard curves
- Melt curve analysis of primer design
- Genotyping
Spectrophotometers
NanoDrop 2000
UV/Vis spectrophotometer for the quantification of DNA, RNA and protein samples using small volumes (0.5-2.0 ul). Detection range of 2 ng/ul-15,000 ng/ul for dsDNA and 0.1 mg/ml-400 mg/ml for BSA. Xenon flash light source with wavelengths spanning 190 nm-840 nm.
Potential applications:
- Quantification of DNA from plasmid preparations, genomic isolation and PCR reactions.
- Measurements of RNA concentration.
- Quantification of protein concentrations.
BioTek Synergy2 Microplate Reader
BioTek Synergy2 microplate reader is a multimodal UV/Vis spectrophotometer capable of absorbance, fluorescence and luminescence based assays for standard multiwell plate formats (6 to 384-wells). The Functional Genomics Core Facility system has the dual reagent dispenser module for controlled addition to compounds during analysis. Contact Functional Genomics Core Facility manager for filter sets available for use.
Potential applications:
- Protein quantification via Bradford.
- Cell viability assays via absorbance, fluorescence and luminescence.
- Readouts of transcriptional reporters through fluorescence and luminescence.
Gel Imaging
Licor Odyssey Fc
Licor Odyssey Fc imaging system equipped with 600, 700 and 800 nm scan channels. Capable of dual-color imaging of western blots in the 700 and 800 channels. 600 nm channel for detection of DNA stained with the SYBR family dyes. Image Studio acquisition software can be used to quantify band intensities for comparisons of individual lanes.
Applications:
- Western blot imaging
- DNA gel imaging
- Analysis of gel images
Microscopes
Olympus SZX16 stereomicroscope
Olympus stereomicroscope for low-level magnification of tissues, organisms and materials. Magnification wheel from 0.7-11.5X along with a 10X magnification eyepiece. This microscope is set up for both transmitted and reflected light microscopy. Additionally, we have an LED-light source for epifluorescence imaging using FITC and RFP filter cubes. Camera is interfaced with a DP71 digital camera and cellSens for image acquisition.
Potential applications:
- Dissection or manipulation of fine tissues.
- Fluorescence imaging of tissue or transgenic organisms.
- Imaging of surface details by reflected light microscopy.
Olympus Bx53 upright microscope
The Olympus Bx53 upright microscope is equipped with 5X, 10X, 20X and 40X air objectives, as well as a 100X oil-immersion objective for high magnification imaging. The Bx53 microscope is equipped for differential interference contrast imaging with the 10, 20 and 40X objectives and phase contrast with the 100X objective in addition to standard Brightfield capabilities. This microscope is also equipped with the X-Cite LED illumination source for epifluorescence with DAPI, GFP, YFP and TRITC filter cubes. For image acquisition this microscope is interfaced with a DP80 digital camera and cellSens image acquisition software.
Potential applications:
- Brightfield imaging of histological slides.
- Phase and differential interference contrast imaging.
- Fluorescence imaging of DAPI-, GFP- and RFP-based fluorophores.
Olympus IX70 inverted microscope
The Olympus IX70 inverted microscope is readily equipped for Brightfield, phase contrast and epifluorescence imaging. This microscope is equipped with 10, 20 and 40X air objectives. The inverted objectives allow for easy access to samples making it ideal for imaging cells in plates or dishes. A mercury lamp source is used for epifluorescence imaging coupled with DAPI, GFP and RFP filters. A DP73 digital camera captures images in conjunction with the cellSens acquisition software.
Potential applications:
- Brightfield and phase imaging of cells in plates or dishes.
- Fluorescence imaging of cells in culture to validate treatments or transfections.
Olympus FV1200 confocal microscope
The Olympus FV1200 system provides high-resolution imaging and optical sections through pinhole rejection of out of focus light. The FV1200 system is equipped with 405/458/488/515/559/635 laser lines to excite the majority of available fluorophores and fluorescent proteins. For emissions detection, the system is equipped with two variable band-pass filters to enable flexible emission collection for the first two detectors. The system also has a third detector with a standard bandpass filter for up to three-channel simultaneous imaging. A transmitted light detector also enables the collection of Brightfield images. 4X, 10X, 20X and 40X air objectives, as well as a 60X oil-immersion objective offer a range of magnifications for imaging. Inserts for both slides, dishes and multiwell plates.
Potential applications:
- Optical sectioning and 3D imaging.
- Spectral unmixing and autofluorescence identification with lambda scan.
- Short-term time lapse imaging.
Manufacture's Manuals:
- User's manual set (full version)
- User's manual quickstart for the IX81 Microscope
FGCF User Protocols:
- FV1200 Start-up
Leica LIAchroic STELLARIS 5
The Leica LIAchroic STELLARIS 5 confocal system provides high-resolution imaging through pinhole rejection of out-of-focus light and can further increase resolution using the included Lightning deconvolution software, resulting in super-resolution imaging of samples. This system is equipped with 405/488/514/559/638 laser lines for excitation of most fluorophores and fluorescent proteins. Available objectives include 5X, 10X and 20X air objectives and both 40X and 60X oil-immersion objectives for high-resolution imaging. The scan head is equipped with 3 HyD spectral detectors for flexible collection of emissions. The system is also equipped with a stage-top incubator for environmental control enabling longer-term live cell imaging. Improved image acquisition speed makes the Leica ideal for imaging large Z-stacks or performing large imaging stitching of multiple fields.
Potential applications:
- High-resolution imaging and super-resolution with lightning deconvolution.
- Long-term live cell imaging.
- Large image stitching.
Nikon Ti2 inverted widefield fluorescence microscope
Nikon Ti2 widefield fluorescence microscope equipped with an 8-line LED excitation system 390/440/475/510/555/575/635/747 to hit virtually all fluorophores and fluorescent proteins. Equipped with 10X, 20X and 40X air objectives with a 0.95 NA on the 40X objective. Full-enclosure incubator for environmental control and live-cell imaging without interference from room lighting. Perfect focus system to ensure no focal drift over time. Polygon DMD for precise photostimulation or optogenetic approaches. Orca Fusion-BT sCMOS camera for image capture with large dynamic range and low noise. NIS-elements software equipped with JOBS for complex imaging experiments.
| Imaging duration | Rate |
|---|---|
| 0-4 hours | $15/hour |
| 4-24 hours | $60 daily maximum |
| 24-48 hours | $45 daily maximum |
| 48-72 hours | $30 daily maximum |
| 96+ hours | $15 per additional day |
Potential applications:
- Live cell imaging for long durations.
- Imaging fluorescent proteins not ideal for confocal applications due to off-peak excitation.
- Photostimulation and optogenetics.
Centrifuge
Beckman OPTIMA 130K Ultracentrifuge
The Beckman OPTIMA 130K Ultracentrifuge is equipped with MLS-50, TLA-120.2 and MLA-55 rotors for high-speed centrifugation needs.
The day-to-day operations of the SDSU Functional Genomics Core Facility is currently managed by a full-time facilities manager Jenna Parliament. The Functional Genomics Core Facility coordinator, Ryan Hanson, is responsible for supervising and for interpreting and implementing policies established by the Functional Genomics Core Facility governing body.
The Functional Genomics Core Facility advisory committee provides oversight into the implementation of new rates and policies, feedback on the overall management of the facility and assists in the identification and prioritization of research needs for new facility equipment.
Committee members are selected from major departmental users of the Functional Genomics Core Facility in association with the facility coordinator and the core research support facilities director.
- National Institutes of Health Centers of Biomedical Research Excellence Award No. P20GM135008
- National Science Foundation EstabÂlished Program to StimÂuÂlate ComÂpetÂiÂtive Research Grant No. 0091948
- Center of Excellence in Drought Tolerance through the South Dakota 2010 Initiative
- SDSU College of Agriculture, Food and Environmental Sciences
- South Dakota Agricultural Experiment Station
- Department of Biology and Microbiology
- Department of Pharmaceutical Sciences
