The GC3F houses a variety of instruments to assist you during the genomic sample prep process. Some instruments are only available with a reservation.
Liquid Handling
Ranin Liquidators
Like a manual hand-held pipette, but with 96 channels to pipet into all wells of a 96-well plate at once. We have a 20ul and 200 ul model, as well as an electronic version with swappable 20ul, 200ul, and 1000ul heads. These instruments use specialized tips which we can sell to UO users at-cost.
The Liquidators can be reserved through iLab.
Hamilton Vantage
Ultra-flexible robotic liquid handler, equipped with 8 single channels and a 96-block head for fast and flexible sample prep. Our deck has two independent chillers and a heater-shaker module to enable essentially any prep you want to automate.
The Hamilton can be reserved through iLab. Contact genomics@uoregon.edu for training.
Centrifuges
Eppendorf 5430 Plate Centrifuge
This plate spinner has a small footprint and is fitted with a rotor that allows you to quickly spin down your 96-well plates (with up to 1 mL capacity). Max speed of 17,500 rpm / 30,000 rcf.
No reservation required. Contact us at genomics@uoregon.edu for spins >20 mins.
Eppendorf 5417R Refrigerated Microcentrifuge
Temperature control from –9 to 40°C and “Fast Cool” function cools from ambient to 4°C in under 20 minutes. Max speed of 25,000 rcf and capacity of 30 1.5 mL microtubes.
No reservation required. Contact us at genomics@uoregon.edu for spins >20 mins.
Beckman Coulter High-speed Refrigerated Centrifuge
Beckman Centrifuge can be reserved for spins >10 mins in iLab.
SpeedVac Centrifugal evaporator
Used for sample concentration and drying using a combination of centrifugal force, heat and vacuum by connecting to a cold trap and vacuum source. By simply switching out the rotor, it can be used to spin either 1.5 mL microtubes or 96-well plates.
No reservation required.
Tissue Homogenization
TissueLyser
Variable-speed probe homogenizer for gentle tissue dissociation. Uses disposable plastic probes for ease of use.
No reservation required.
GenoGrinder
Rapid cell disruption, cell lysis, and tissue homogenization through bead beating for fast and efficient extraction of nucleic acids, proteins and other molecules of interest. The Geno/Grinder operates at speeds of up to 1750 strokes/minute and up to 20 minutes in duration. It is equipped with an adjustable clamp that accommodates a full range of sample vials:
- Up to 48 x 1.5 mL microtubes
- Up to 16 x 50 mL conical tubes
- Up to 6 x deep-well titer plates
No reservation required.
DNA Shearing
Megarupter 2
Reproducibly fragment HMW DNA to a target size of 3kb-75 kb. Shearing performance is independent of the source, concentration, temperature, or salt content of a DNA sample.
No reservation required.
Covaris M220 sonicator
Covaris transmits acoustic energy at ultrasonic frequencies and very short wavelengths to shear DNA to fragment sizes between 150bp and 5kb. The process is isothermal, non contact, and quiet, and the instrument is very easy to operate. Accomodates sample volumes of 15 µL, 50 µL, or 130 µL in specialized tubes that we stock in house, and can process up to 5 µg of DNA per tube.
The Covaris can be reserved in iLab.
Size Selection
BluePippin
Automated size selection of nucleic acid fragments anywhere between 50 and 50,000 bp in size. Easier, safer, and more reproducible than traditional agarose gel extraction protocols involving a UV illuminator and a razor blade. We sell cassettes to UO users at-cost as needed.
The BluePippin can be reserved in iLab.
Omega Beads
Omega Bio-Tek's TotalPure NGS Mag-Bind Beads can be used to purify and size-select both DNA. UO researchers can purchase aliquots of these beads from the GC3F for $7 per mL. We have run a full series of tests to characterize their DNA size selection properties (view the evaluation here, courtesy of Maggie Weitzman).
Omega Beads can be purchased through the iLab request system.
Quantification
Nanodrop
The GC3F houses two Nanodrop instruments (the 1000 and the 2000) for quantification of proteins and nucleic acids. Thermo Scientific's patented sample retention system allows for the analysis of 1-2 µl samples, without the need for cuvettes, capillaries, or loading dyes.
No reservation required.
Qubit 3.0 and Qubit Flex
Benchtop fluorometers for measuring DNA, RNA, and protein concentration by reporting a fluorescent due that emits signal only when bound to target, minimizing the effects of contaminants. Qubit 3.0 accepts 0.5ml tubes and Qubit flex accepts strip tubes.
No reservation required.
SpectraMax
Measures UV and visible absorbance, fluorescence intensity measurements, glow luminescence, time-resolved fluorescence, fluorescence polarization, and HTRF. It accepts cuvettes or plates.
SpectraMax can be reserved through iLab.
QuantStudio 3
qPCR machine equipped with a 96-well block. Features easy-to-use touchscreen programming, optional web-based data management, and pre-programmed assays.
QS3 can be reserved through iLab.
QuantStudio 5
qPCR machine equipped with a 384-well block. Features easy-to-use touchscreen programming, optional web-based data management, and pre-programmed assays.
QS5 can be reserved through iLab.
BioRad CFX96
This six-channel (five colors and one FRET channel) real-time PCR instrument combines advanced optical technology with precise temperature control to deliver sensitive, reliable detection for singlexplex or multiplex reactions. Includes High Resolution Melt (HRM) curve analysis software.
BioRad CFX96 can be reserved through iLab.
Imagers
Typhoon
A GE Amersham Typhoon imager is available in the facility for scanning gels, blots, microscope slides, microtiter plates, tissue specimens, and more! This new laser scanner is designed for versatile imaging and precise quantitation of fluorescent, colorimetric, and radiolabeled proteins and nucleic acids.
- 4 types of imaging:
- RGB & IR fluorescence
- Luminescence
- Phosphor (RI) imaging
- Densitometry (OD)
- Illuminates with scanning lasers & detects light with photomultiplier tube (PMT)
- Equipped with 488nm, 532nm, 635nm, 685nm, and 785 nm lasers
- Emitted light is detected & amplified with a PMT, providing superior signal sensitivity
- Can accomodate very large samples, up to 40 cm x 46 cm in size. This large scanning surface also means that multiple gels/plates/etc. can be imaged & analyzed simultaneously.
- Provides max image resolution of 10 µm
The Typhoon is housed in the Imaging Facility and can be reserved in iLab.
Licor Odyssey
Analyzes both chemiluminescence and near-infrared fluorescence such as Western blots, agarose gels, SDS-PAGE gels, Coomassie protein gels, RNAi analysis, and other assays. It uses 2-channel near-infrared fluorescence (green & red signals), which allows 2 proteins to be detected in the same sample lane without stripping and re-probing. Direct detection of near-infrared fluorescence signals is performed using secondary antibodies labeled with IRDye NIR fluorescent dyes, or other commercially available dyes such as SYBR Safe, SYBR Green I, SYTO 60, and other popular DNA stains.
No reservation required.