eagle-i University of Alaska FairbanksUniversity of Alaska Fairbanks
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DNA Core Laboratory

Director: Leigh, Mary Beth, Ph.D.

Summary:

A staffed facility intended to keep UAF at the "cutting edge" of nucleic acid analysis in evolutionary biology, molecular biology, and wildlife and fisheries management. The Core Facility provides nucleic acid sample analysis, and maintenance and support for molecular instruments (some of which may be too expensive for individual labs to own) for both UAF and outside users.

Affiliations:

People:

Resources:

Instruments

  • ABI 3100 genetic analyzer ( DNA sequencer )

    The ABI 3100 Genetic Analyzer is used for fragment analysis and standard sequencing usually with a 50cm array with polymer 6 (Pop6), which gives sequence reads up to about 500-700 base pairs. Longer reads are run either on the 3130xl with Pop7 (up to 900bps) or on the 80cm array (800-1000 bps) which takes twice as much time and polymer. Capillary array system for DNA sequencing and genotyping, with syringes.

  • ABI 3130xl genetic analyzer ( DNA sequencer )

    16 capillary array system for DNA sequencing and genotyping, with pump. The ABI 3130xl Genetic Analyzers is basically an upgraded 3100 with a pump system instead of syringes which allows it to run Pop7 as well as Pop6. Polymer 7 can be run on the 50cm array and gives sequence reads up to about 900+bp instead of only 500-700bp that are possible with Pop6. This means it can collect longer sequences in the same amount of time using a similar amount of polymer per sample. The 80cm array on the other hand takes twice as long and uses twice the polymer for only 800-1000+ bases.

  • ABI PRISM 7900HT sequence detection system ( Real-time PCR machine )

    The ABI 7900 HT system offers Real-Time detection (i.e., quantification) of the Polymerase Chain Reaction (PCR) or Endpoint assay measurements of PCR. The 7900 is built for high throughput with the capability for 96 or 384 well block format. The blocks are exchangeable (If you need the block changed contact Ian). The instrument is also compatible with an automated plate loader for high throughput (we do not have this addition). The SDS 2.1 software manages and analyzes data for SNP genotyping and gene expression, with a choice between Absolute or Relative quantitation methods for gene expression. Two types of chemistries are used to detect PCR products using the Sequence Detection Systems (SDS) instrument, TaqMan and SYBR Green.

  • Agilent 2100 Bioanalyzer ( Microfluidics platform )

    The Agilent 2100 Bioanalyzer is applied lab-on-a-chip technology designed to analyze RNA, DNA, proteins and cells. It can perform electrophoretic quantification of 12 samples in 30 minutes, using 1-4ul of sample, with as little as 50pg of RNA. This instrument is used to generate standardized QC values for RNA and assigns an RNA Integrity Number (RIN) to samples, allowing easy determination of RNA quality with reproducibility and comparability of results between samples and labs. This is often used before microarray or qPCR experiments. It can also be used for measuring size and concentration of DNA fragments in PCR/mPCR, multiplexed PCR and RT-PCR products as well as for protein size, purity and concentration. The digital data is easy for archiving and comparison, it also allows a variety of viewing options, including a gel-like format. Chemistries for this instrument come in RNA, DNA or Protein kits specially designed for certain size ranges or concentrations. For more information on kits the Agilent website is very useful. The Core Lab also has information available.

    The instrument in the Core Lab is not equipped for analysis of cells using Flow Cytometry and would require an upgrade in order to allow this function.

  • Alpha Innotech AlphaImager 3400 gel documentation system ( Gel imaging system )

    The AlphaImager is a multi-function gel and image detection system that is equipped with a 12-bit CCD camera. It saves 16-bit files and has a host of software features that enhance image readability. Notes, labels, arrows, lines, and other drawing tools are easily added to an image. There are four auto-exposure modes, or complete manual control, ensuring customization of exposure and image capture. A movie mode allows for a series of up to 50 images to be taken, with each frame capture capable of different time intervals and exposure modes. The clarity of the image can be modified through conversion of a positive image to negative, applying digital filters, using false color maps, or adjusting the auto or manual contrast. A number of automated features are available, including:

    Molecular weight calculations
    Rf determination
    1-D Lane and 2-D Spot densitometry
    Quantitative PCR
    Microtiter plate reading
    Object distance measuring
    Gel scoring
    Colony counting
    Lane/band detection with smiling correction

  • Amersham Typhoon 9200 Imager ( Gel imaging system )

    The Typhoon instrument is a variable-mode imager that produces digital images of radioactive, fluorescent, or chemiluminescent samples. The Typhoon system consists of an instrument, instrument control software, and a variety of accessories. Image Quant Software includes: FragmeNT Analysis V1.2, Gene Sight V3.2, ImaGene V3.2, Image Quant V5.2, IQTools V2.2, FluorSep V2.2, and Clone Tracker V2.0.

    The Typhoon scans and processes samples in the following way:
    - Red laser illuminates each one-pixel section of an exposed storage phosphor screen, the phoshphor screen emits blue light.
    - When the green laser (532 nm) or the red laser (633 nm) illuminates each one-pixel section of a fluorescent sample, the fluorochrome emits light with a characteristic spectrum.
    - The chemiluminescent sample emits light with a characteristic spectrum.
    - Multilabel-excited mode-Creates an image from a sample labeled with up to four fluorescent dyes. The dyes can be excited by one or two of the laser wavelengths.

  • BD FACSAria ( Flow cytometer )

    The FACSAria flow cytometer is a high speed cell and particle sorter.

    If you have a project you would like to run on this instrument contact the Core Lab. The Core Lab Coordinator/Technician is a certified BDFACSAria Operator, and is happy to discuss project possibilities with potential users.

  • Beckman Coulter Allegra 21R centrifuge ( Tabletop centrifuge )

    There are two rotors for this centrifuge, one can hold 36x1.5-2.0ml tubes, and spin at a maximum rpm of 14,000/ 19,280rcf. The other rotor is a swinging bucket that can hold up to 4x96 well plates, and spin at 3,000rpm/1,100rcf. Temperatures can be set between -20 to +40 C and run times can be programmed for up to 10 hours.

  • Beckman Coulter Biomek 2000 laboratory automation workstation ( Liquid handler )

    The Biomek 2000 is a liquid handling robot. It has flexibility so users can write their own programs for PCR set-up, DNA extractions, etc. or it can run company made programs such as setting up gene chip arrays for the Ciphergen. Our instrament has the additional shaker and vacuum attachements. The Biomek can move liquid amounts down to 2ul with only 3% error.

  • Beckman Coulter Microfuge 18 microcentrifuge ( Microcentrifuge )

    Holds 24x1.5/2.0ml tubes and spins up to 14,000rpm/18,000rcf. Programmable timer for 0-30 minute runs.

  • Beckman Coulter Optima L-100XP ultracentrifuge ( Ultracentrifuge )

    Service contract. Large, temp-controlled ultracentrifuge. Rotors: 70.1 Ti fixed angle, 50.2 Ti fixed angle, NVT 100 (near vertical), SW 28 Swinging bucket.

  • Bio-Rad CHEF Mapper PFGE (Pulsed Field Gel Electrophoresis) XA System ( Pulsed-field gel electrophoresis system )

    Gel matrix used to separate very high molecular weight DNA (>20 kb). Includes internally programmed conditions for optimizing separation of DNA between any two sizes.

  • Eppendorf AG 5417R centrifuge ( Centrifuge )

    Pre-PCR centrifuge, tubes of plates. This centrifuge is can spin up to 16,400rpm with a temperature range of -9C to +40C. The rotor bowl can be cooled from ambient to 4C in less than 20 minutes using the fast cool function. Rotor speed is displayed in rpm or RCF. There is a soft start/stop feature to protect samples. Automatic rotor detection displays maximum permissible speed. The current rotor holds 30X1.5/2.0 microtubes with a maximum of 14,000 rpm. At this time we only have one rotor.

  • Eppendorf AG VacuFuge 5301C concentrator ( Centrifuge )

    SpeedVac centrifuge; hold 48 tubes and two 96 well plates.

  • Eppendorf AG VacuFuge 5301P vacuum dryer ( Vacuum dryer )

    SpeedVac centrifuge; hold 48 tubes and two 96 well plates.

  • Illumina BeadStation 500X ( Bead array reader )

    The Illumina BeadStation 500X supports Gene Expression profiling of focused sets of genes and whole genomes. It enables a wide range of sample throughput (16-192 samples/day) and broad experimental scale (6000-300,000 genotypes per day). The Bead Array Reader is a confocal scanner with < 1 micron resolution for use with Sentrix® Array Matrices and Sentrix® BeadChips. The Core Lab also has the Illumina Hybridization oven with BeadChip Hyb wheel model 5420.

  • Kendro Sorvall RC-5C Plus Super Speed Centrifuge ( Centrifuge )

    Service contract, large, temp-controlled floor centrifuge. Rotors: SA-512, SA-600, SCL-3000, HS-4.

  • Millipore Milli-Q Synthesis System ( Water purification system )

    Ultrapure water system; 18.2 Mega Ohm, UV.

  • MJ Research PTC-225 TetradEngine A ( Thermal cycler )

    The Core Facility has two MJ Research PTC-225 DNA Engine Tetrad thermal cyclers that are gradient enabled and have heated lids. The temperature can range from –5 to 105 º C with a maximum ramping speed of 3º C per second. There are three 48/48 dual alpha blocks that will hold 48x0.2 ml tubes, or 48 well PCR plates, and each can run independent programs. There are also five Alpha units capable of holding 96x0.2 ml tubes, or one 96 well plate each.

    The 96 well Alpha units can run a gradient of up to 24 º C across a block, with 12 different temperatures. Programs can be created and stored in individual lab folders on the instrument.

  • MJ Research PTC-225 TetradEngine B ( Thermal cycler )

    The Core Facility has two MJ Research PTC-225 DNA Engine Tetrad thermal cyclers that are gradient enabled and have heated lids. The temperature can range from –5 to 105 º C with a maximum ramping speed of 3º C per second. There are three 48/48 dual alpha blocks that will hold 48x0.2 ml tubes, or 48 well PCR plates, and each can run independent programs. There are also five Alpha units capable of holding 96x0.2 ml tubes, or one 96 well plate each.

    The 96 well Alpha units can run a gradient of up to 24 º C across a block, with 12 different temperatures. Programs can be created and stored in individual lab folders on the instrument.

  • Molecular Devices Analyst AD (96-394) ( Fluorescence and luminescence assay detection system )

    Assay development system with four modes, fluorescence, luminescence, absorbance, and Epi-absorbance. The instrument can be programmed to use either a xenon-arc lamp as a continuous light source, or a xenon flash lamp. The machine has a filter wheel that holds eight 25-mm diameter filters, has one dichroic mirror, a 50:50 beam splitter, two sets of polarizers [S (horizontal) or P (vertical) orientation], and a Fluorescence and luminescence PMT (Photomultiplier tubes).

    There are seven optical measurements:

    Fluorescence Intensity (F)
    High Efficiency Fluorescence Polarization (HEFP)
    Time-Resolved Fluorescence (TRF)
    Luminescence (L)
    Focused Luminescence (FLUM)
    Absorbance (A)
    Epi-Absorbance (EA)
    Software: Criterion Host and SoftMax Pro

  • Molecular Devices SpectraMax Plus 384 ( Spectrophotometer )

    The SPECTRAmax Plus 384 spectrophotometer provides measurements of a variety of analytes including proteins, nucleic acids, and other molecules. It can measure the optical density in a cuvette, 96 or 384 well plate over a specified period of time (kinetic), single point in time (endpoint), or over a selected wavelength range (spectral scan). The SOFTmax Pro V4.0 can take data from multiple readings in each well or individual readings in each well. The SPECTRAmax can shake samples before each reading and the chamber temperature can be regulated between 4° C and 45° C.

  • NanoDrop ND-1000 Spectrophotometer ( Spectrophotometer )

    Used for DNA and RNA quantification. The NanoDrop ND-1000 is a full-spectrum (220-750nm) spectrophotometer that can measure concentrations in 1-2ul of sample with good accuracy and reducibility. It has the capability to measure highly concentrated samples without dilution (75x higher concentrations than can be measured in a standard cuvette spec).

    To operate the NanoDrop you pipette 1 or 2ul of sample onto the end of a fiber optic cable (receiving). A second fiber optic cable (source) is lowered down on an arm and causes the liquid to form a column between the two cables. A pulsed xenon flash lamp provides the light source and a spectrometer using a linear CCD array analyzes the light after it passes through the sample. A laptop is attached with software that controls the NanoDrop and collects and stores the data at which point you can save the files or print them out.

    The NanoDrop ND-1000 can be used to measure:

    Nucleic acid concentration and quality of nucleic acid samples up to 3700ng/ul (dsDNA) without dilution.
    Fluorescent dye labeling density of nucleic acid microarray samples
    Purified protein analysis (A280) up to 100 mg.ml (BSA)
    Bradford Assay analysis of protein
    Cell density measurements
    General UV-Vis spectrophotometry

  • OHAUS Adventurer Balance A2140 ( Balance )

    The Ohaus Adventurer Balance has a maximum capacity of 210g, and reads to 0.1mg. The balance pan is covered by a three door draft shield to prevent air currents from affecting the accuracy. It can be set to the following units: g, kg, mg, ct, N, lb, oz, ozt, GN, dwt, mo, m. Be careful if the instrument has been moved, as it may need to be re-leveled.

  • Qiagen BioRobot 8000 ( Liquid extraction robot )

    The Qiagen BioRobot 8000 is a fully automated, software-controlled, modular workstation. The BioRobot is capable of liquid handling for DNA isolation, normalization, PCR prep, clean up, plasmid-prep, etc. It is accurate down to 5ul and flexible enough to write your own protocols. Many of the Qiagen kit protocols can be run on this instrament. The Qiasoft 4.1 Operating System operates under Microsoft Windows NT.

  • Qiagen QIAcube Liquid Handling Platform ( Liquid extraction robot )

    The QIAcube processes QIAGEN spin column based kits (DNA, RNA, protein), for automated, low-throughput sample prep. No change of purification chemistry is required. Up to 12 samples can be processed per run.

  • Ranin Electronic Pipette ( Electronic repeater pipette )

    Repeater pipettes, 1-10, 2-20, 20-200, 100-1000.

  • Ranin Multi Channel Electronic Pipettes ( Multichannel electronic pipette )

    8 channel, E8-10, E8-20, E8-200, E8-1200.

  • Savant SpeedVac DNA 110 ( Vacuum dryer )

    Speed Vac centrifuge, tubes only. Can hold up to 36x 1.5/2.0ml tubes.

  • Sigma 6K15 Centrifuge ( Centrifuge )

    This is a high volume tabletop centrifuge that can operate at speeds of 100-15,000rpm, temperatures of -20C to +40C, and is programmable for all parameters. The memory can hold up to 50 programs. A single knob controls the centrifuge using the LCD display which also shows the rotor/bucket combinations along with their max speed and gravitational field. There are separate touch keys for start, stop, and lid. An automatic rotor identification prevents rotor over-speeding. The rotors are stored in the drawer below the instrument.

  • Steris Amsco Century Autoclave (Pre-PCR) ( Autoclave )

    Autoclave for "clean" things. Pre-PCR, glassware, tips, clean media, buffers, saline solution, pure water. Owned generally by IAB/Facilty services Not located in DNA Core Lab or owned by them.

  • Steris Amsco Renaissance Autoclave (Post-PCR) ( Autoclave )

    Autoclave for post-PCR, soil (anything that could cause contamination of samples). Owned generally by IAB/Facilty services; not located in DNA Core Lab or owned by them.

  • Transgenomic WAVE DHPLC ( Denaturing high-performance liquid chromatography instrument )

    DHPLC and fragment collector with many moduals. Fees apply.

  • UVP Laboratory Products HL-2000 Hybrilinker ( Hybridization station )

    Hybridization oven and UV crosslinker for nucleic acid hybridization.

  • VirTis Lyo-Centre 7.0-ES lyophilizer ( Lyophilizer )

    Bench Top Freeze Dryer.

  • VWR Galaxy Mini Centrifuge ( Microcentrifuge )

    Microcentrifuge for strip tubes. Holds two strips, or 16 individual 0.2ml microtubes and spins up to 6,000rpm. The Galaxy also has a little rotor that can hold 6x1.5/2.0ml tubes.

  • VWR SR601C Symphony Meter ( pH meter )

    VWR SympHony Meter SR601C: This meter can measure pH from -2.000 to 19.999. The Core Lab has a pH Posi-pHlo Ag/AgCl glass electrode and an ATC (automatic temperature compensation) epoxy temperature probe. Autocalibration is possible with 1 to 5 buffers.

Protocols

Services

  • 96-well sequencing plates purchase service ( Support service )

    Lab buys ABI 96-well sequencing plates in bulk and sells to researchers for their convenience.

  • Big dye terminator V3.1 purchase service ( Support service )

    Lab buys Big Dye in bulk and sells to researchers for their convenience. There is Big Dye buffer available at no extra cost if you purchase Big Dye from the Core Lab.

  • Fragment Analysis (microsats, AFLP, T-RFLP) ( Material analysis service )

    The user provides premixed samples (PCR product , size standard and HiDi Formamide) in a 96-well plate. The Core Lab tech then loads and runs the samples. All PCR supplies and size standards are provided by the user. HiDi Formamide is provided by the Core Lab at no extra cost. The Core lab only accepts pre-mixed fragment samples for fragment analysis. It does not affect the price if markers are multiplexed in each well; only the number of wells matters. The User enters sample names into the computer, otherwise the samples are labeled only by well number. Ask in the Core Lab for a sample sheet template if you want to enter names on your computer.

  • Real-time PCR training service ( Training service )

    The user gets an introduction to the ABI 7900HT machine and software from a Core Lab Technician. Once this training is completed the user is free to sign-up on the calander and use the Real-Time PCR machine.

  • Sample sequencing service ( Material analysis service )

  • Sequencing service ( Material analysis service )

    Service includes clean PCR or plasmid samples for cycle sequencing, Sephadex clean-up, and sequencing.

  • SpectraMax spectrophotometer plates purchase service ( Support service )

    Lab buys 96-well UV Greiner plates in bulk and sells to researchers for their convenience.

Software

  • ABI DNA Sequencing Analysis Software ( Software )

    Analyze sequence data, and trim, call and edit bases. Check sequence quality, and assign quality values for bases called using color coding.

  • ABI Peak Scanner ( Software )

    DNA fragment analysis software. Sorts fragments according to size, calculates the exact size of fragments, and provides a separation profile.

  • ABI Primer Express ( Software )

    Oligonucleotide design program.

  • ABI SeqScape ( Software )

    "Applied Biosystems SeqScape® software v2.7 is designed for reference based analysis such as mutation detection and analysis, SNP discovery and validation, pathogen sub-typing, allele identification, and sequence confirmation. This product is also integrated for use with VariantSEQr™ Resequencing Set."

  • ABI Sequence Scanner ( Software )

    Free software from ABI for viewing, editing, printing and exporting sequence data.

  • GeneMapper ( Software )

    Fragment analysis software. Useful for SNP detection and analysis of Microsatellite, AFLP, TRFLP, etc. data.

  • ImageQuant TL ( Software )

    General image analysis software for 1D gels, arrays and colony counting.

  • Sequencher ( Software )

    Edit, assemble and analyze your DNA sequences. SNP detection, Restriction Mapping, sequence data confidence values, and GenBank import or export capabilities. In version 5, Next Generation Sequencing data is supported. This is the network version with two seats, which means if 2 computers are logged into the website, no more may access Sequencher.

  • SoftMax Pro ( Software )

    "An all-in-one data acquisition and analysis solution to get from reader set-up to results faster.

    SoftMax® Pro Data Acquisition & Analysis Software serves as the user interface to the popular EMax®, VMax™, Gemini™, and SpectraMax® Microplate Readers. Users are able to customize reader settings through the software to take advantage of unique reader technologies that improve the quality of assay data such as: temperature-independent pathlength correction for absorbance measurements and automatic gain correction for fluorescence."


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Last updated: 2014-09-24T13:59:33.377-05:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016