Functional Genomics Core Facility
The SDSU Functional Genomics Core Facility (SDSU-FGCF) exists to facilitate interdisciplinary gene function research and training in viral, bacterial, plant and animal systems. This is accomplished by providing researchers with: 1) access to expensive, cutting-edge technologies (i.e. instrumentation) for functional genomics research at a minimal cost. 2) Training and support on the optimal uses of these technologies. 3) An opportunity to assist with and influence future purchases of functional genomics-related equipment.
Location
The primary SDSU-FGCF suite is located in the lower level (Room 047) of the Edgar S. McFadden Biostress Laboratory (SNP) and consists of three laboratory rooms containing various equipment necessary for studying the functions of genes.
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The day-to-day operations of the SDSU-FGCF is currently managed by the FGCF coordinator (Dr. Ryan Hanson).
How to obtain FGCF access
The FGCF is accessible 24/7 for registered users through keycard based access. All SDSU faculty and students can become registered users. Contractual arrangements can also be made for students, faculty and staff from other universities and for industry employees to become registered users. To gain access to the rooms and to use the equipment, you must first send Ryan Hanson an email providing the following information:
- Last name
- First name
- Email address
- Department
- Phone number
- SDSU ID number
- Person to be billed
Approximately one to two days after submitting this information, your SDSU student/faculty/staff ID card will be activated so that you can open the core's swipe-card door-system into the core suite. Your FGCF user name and password will be sent to you via email.
How to reserve and access equipment
To use any equipment in the FGCF, you must type your Pharos user name and password into the computer associated with the instrument. There is a pre-set maximum usage time for each instrument and the computer will shut down at the end of the allotted time. It will give you a short warning before shutting down, so it is very important to save any open computer files at that time. To end the billing period prior to the allotted time, you must log off of the computer (select "Start" then "Log Off"). Do not save any data on the computers in the FGCF because they will turn themselves off each night and all of the files saved during that day will be deleted.
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 schedule a time-slot to use each instrument online.
The FGCF is primarily a user-run facility. As such, researchers are responsible for providing their own labor. Training is available upon request from the facilities manager, Liping Gu. Additionally equipment manuals for many pieces of equipment is also available upon request. Instrument maintenance is supported through user fees and associated prices.
Acknowledging FGCF use
Proper acknowledgement of the use of FGCF 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 FGCF 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 Number 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.
User Fees
- Users must supply all supplies and reagents needed during the operation of these instruments.
- To calculate prices for non-university 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 based on Pharos login down to the minute.
| Equipment | Location | Cost ($/hr) |
|---|---|---|
| ABI 9700 Thermocyclers | SNP 047 | $1.50/run |
| ABI Veriti Gradient Thermocyclers | SNP 047 | $1.50/run |
| QuantStudio 6 Flex Real-Time PCR System | SNP 047 | $16/run |
| LI-COR Odyssey ® Fc Imaging System | SNP 047 | $13/hr |
| Bio-Rad ChemiDoc XRS Imaging Station | SNP 047 | $9/hr |
| BioTek Synergy 2 Multi-detection Microplate Reader | SNP 047 | $12/hr |
| Octet R8 Bio-layer Interferometry | SNP 047 | $40/hr |
| Nandrop ND-2000 Spectrophotometer | SNP 047 | $9/hr |
| Agilent GCMS 5975 Diffusion System | SNP 047 | $21/hr |
| Beckman OPTIMA 130K Ultracentrifuge with MLS-50, TLA120.2 and MLA-55 rotors | SNP 047 | $1.80/hr |
| Olympus BX53 Upright Microscope with camera | SNP 047 | $8.40/hr |
| Olympus IX70 Inverted Microscope with camera | SNP 047 | $8.40/hr |
| Olympus Fluoview 1200 Confocal Microscope | SNP 047 | $21/hr |
| Olympus SZX16 Epi-Fluorescent Stereo Microscope with camera | SNP 047 | $8.40/hr |
| Leica LiaChroic Confocal Microscope | SAV 313 | $28/hr |
| Nikon Ti2 widefield fluorescence microscope | SAV 313 | $15/hr; see equipment for long-term imaging rates |
| Leica CM1850 UV Cryostat with Cryovac and CryoJane Systems | SNP 047 | No cost: user provides consumables |
| Olympus CUT 4060E Rotary Microtome with accessory for plastic sectioning | SNP 047 | No cost: user provides consumables |
Additional Equipment
The FGCF also offers additional equipment available upon request. This equipment carries no user fee, but the user must supply all associated consumables.
- Bio-Rad PROTEAN IEF 2D Gel Systems
- Agilent 2100 Bioanalyzer
- Bio-Rad Gene Pulser Xcell Electroporation system
- Qubit 3 Fluorometer
The FGCF houses of a variety of equipment to support research needs on campus, ranging from PCR amplification to microscopic imaging. To get information about each instrument select the appropriate drop down menu. For questions about specific equipment or applications, please contact FGCF coordinator Ryan Hanson.
ABI Thermocycler
96-well format thermal cycler with standard temperature range from 4-99°C. Sign-up sheet placed next to instrument.
Potential applications:
- PCR amplification of nucleic acid templates for plasmid design, genotyping or sequencing.
ABI Veriti Gradient Thermocycler
ABI Veriti thermal cycler with 96-well format. Simple touch screen control for setting up cycling programs. Capable of heating gradients for optimizing PCR conditions.
Potential applications:
- PCR amplification of nucleic acid templates for plasmid design, genotyping or sequencing.
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. Touch screen and software based set-up 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.
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 multi-modal UV/Vis spectrophotometer capable of absorbance, fluorescence and luminescence based assays for standard multi-well plate formats (6 to 384-wells). FGCF system has the dual reagent dispenser module for controlled addition to compounds during analysis. Contact FGCF 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.
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
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 DIC 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 DIC imaging.
- Fluorescence imaging of DAPI, GFP and RFP based-fluorophores.
Olympus AX70 upright compound microscope
For questions, please contact Liping Gu, FGCF Manager or FGCF coordinator Ryan Hanson.
Manufacture's Manuals:
- Olympus AX70 Upright Compound Microscope
- Epi-fluorescence attachments
- DIC attachments
- Phase-Contrast attachments
- Olympus DP70 digital camera
FGCF User Protocols:
- Epi-fluorescence attachments
- DIC attachments
- Phase attachments
- Olympus DP70 digital camera
Web Resources:
- Basic digital photography
- Electronic acquisition of microscopic images
- Light Microscopy (microscope primer)
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 IX71 inverted microscope
For questions, please contact Dr. Liping Gu, FGCF Manager or FGCF coordinator Dr. Ryan Hanson.
Manufacture's Manuals:
- Olympus IX71 Inverted Compound Microscope
- Epi-fluorescence attachments
- Phase attachments
- Olympus DP70 digital camera
FGCF User Protocols:
- Epi-fluorescence attachments
- Phase attachments
- Olympus DP70 digital camera
Web Resources:
- Basic digital photography
- Electronic acquisition of microscopic images
- Light microscopy (microscope primer)
- General concepts
- Anatomy
- Phase contrast
- Differential interference contrast
- Fluorescence microscopy (concepts)
- Fluorochrome concepts from molecular expressions microscopy primer
- Table of fluorochromes
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 2 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 3-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 multi-well plates.
Potential applications
- Optical sectioning and three-dimensional 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 pin-hole 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, 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.
| Long-term imaging structure | |
|---|---|
Imaging duration | Rate |
0-4 hours | $15/hr |
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.
Agilent 5975 GC-MS system
Agilent 5975 Gas Chromatograph/Mass Spectrometer
Agilent LC1220 HPLC system
Agilent High-Performance Liquid Chromatography system
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.
Additional equipment available upon request
Additional equipment available upon on request includes the following. Users are expected to provide consumables.
- Agilent Bioanalyzer
- BioRad Gene Pulser Xcell Electroporation System
- BioRad PROTEAN IEF System with PROTEAN Plus Multi-Casting Chamber, PROTEAN Plus Dodeca Cell, PowerPac HC Power Supply
- Qubit 3 Fluorometer
The day-to-day operations of the SDSU-FGCF is currently managed by a full-time facilities manager. The FGCF coordinator, Ryan Hanson, is responsible for supervising Gu and for interpreting and implementing policies established by the FGCF governing body. The FGCF advisory committee provides oversight into the implementation of new rates and policies, feedback on the overall management of the FGCF and assists in the identification and prioritization of research needs for new FGCF equipment. Committee members are selected from major departmental users of the FGCF in association with the FGCF coordinator and the core research support facilities director.
- National Institutes of Health Centers of Biomedical Research Excellence Award No. P20GM135008.
- NSF EPSCoR 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.
