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Plant-Microbe Genomics Facility

Summary:

The Facility, established in 2000, serves the entire Ohio State University as well as the researchers in the state of Ohio and beyond, by providing resources in order to study genomes from DNA sequence to protein activities. Despite our name, the Facility can study any organism's DNA, RNA or protein. The Facility provides 5 major services: 1) DNA Sequencing, 2) Genotyping, 3) Gene Promoter Characterization, 4) Real-time PCR, , and 5) Biomolecular Interaction Analysis. The procedures are designed to provide the opportunity to obtain high quality results at a reasonable cost. This is a cost recovery unit while tours and demonstrations for any group or individual are free. Please explore the website and feel free to contact us in order to learn about how we can assist you.

Affiliations:

Resources:

Instruments

  • AppliedBiosystems 3730 DNA Analyzer ( DNA sequencer )

    An automated, fluorescence capillary electrophoresis instrument that performs Sanger DNA sequencing and DNA fragment analysis in support of the following services: DNA sequencing, Genotyping, and Promoter Characterization.

  • Beckman BioMek FX ( Liquid handling system )

    This robot uses a 96-tip head to do anything any person can do with a pipette. The instrument also includes a tip washing station, heated/cooled stations, and a linear mixer. The FX supports many services at the Facility, e.g. amplicon purification, and can be programed for custom applications for any client.

  • Biacore T100 Bioanalyzer ( Surface plasmon resonance instrument )

    The T100 utilizes surface plasmon resonance to measure interactions (binding constant, association/disassociation rates) between biological molecules in real-time without labels. The instrument is automated and provides temperature control from ambient room temperature to 42C. The instrument is available for client self-use after being trained by Facility staff.

  • BioRad CFX96 real-time System ( Real-time PCR machine )

    The CFX96 is a thermal cycler that can measure fluorescence for 5 separate channels from 96 samples simultaneously. It is most commonly used for quantitative PCR applications in order to measure concentrations of target nucleic acid molecules, but it can be used for other applications such as measuring protein and DNA melting characteristics.

  • BioRad VersaDoc 4000MP Imaging System ( Instrument )

    The 4000MP can image gels or a wide range of objects Imaging with a wide range of wavelengths for the detection of fluorescence, absorbance and chemiluminescence.

  • Tecan SpectraFluor Plus ( Microplate reader )

    The facility has a SpectraFluor Plus (Tecan) that can measure the absorbance, fluorescence, and glow luminescence from samples in a 96-well or a 384-well plate.

    The plate reader has the ability to: (1) measure from 230 to 700nm with the appropriate filter, (2) incubate the plate from room temperature up to 42C, (3) shake the plate in a linear or orbital manner, and (4) perform timed measurements for kinetic analysis

    Currently the reader has the following band pass filters, but additional filters can be purchased if the need arises:
    >Absorbance: 260, 280, 405, 340, 450, 492, 540, 620, 650nm.
    >Excitation or Emission: 360, 430, 465, 485, 535, 590, 595, 635nm.

Services

  • Biomolecular Interaction Analysis ( Access service )

    The facility has a Biacore T100 that can measure the interaction between proteins and proteins, DNA and proteins, metabolites and proteins, as well as other biomolecules that can be anchored to a gold covered chip. The measurements are done in real-time with no labels and utilize surface plasmon resonance (SPR) technology. The T100 can measure concentration, binding specificity, and affinity constants.

    Due to the nature of the studies performed with the T100 the client uses the instrument in order to allow for instant analysis of the results and therefore immediate decisions about the next step or experiment to be done. In order to use the instrument, all clients are required to attend a training session provided by the Facility or the Biacore Basics course offered by GE Healthcare. The training provided by the staff is done at the Facility, takes one to three days and can accommodate up to 2 clients at a time. The client will need to provide all materials and training will utilize the client's samples. An experienced staff member will provide guidance during the initial experiment and the training has a set fee. The training will include: practical use of the instrument, experimental design, and analysis. Please contact the Facility to arrange a training session and begin using the Biacore T100.

    The facility has the following software to aid in the analysis of the data generated by the Biacore T100: Biacore T100 Evaluation Software.

  • DNA Sequencing (Sanger, Capillary) ( Material analysis service )

    The facility uses the 3730 DNA Analyzer from Applied Biosystems, Inc. and BigDye Terminator Cycle Sequencing chemistry. This automated instrument utilizes fluorescent dye labeled nucleotides and provides high volume capabilities, e.g. 384 sequencing reactions in 12 hours, and typically yields 800 to 1000 bases per reaction depending upon the quality and nature of the template.

  • Education ( Service )

    List of Basic Tour Options:
    >Nickel Tour - about 10 to 15 min; brief tour of Facility with a description of the purpose of each instrument.
    >Dime Tour - about 15 to 30 min; nickel tour that also includes examples of data and projects.
    >Dog 'n Pony Show - about 30 to 50 min; dime tour that also includes demonstration of equipment and more details/explanations.

    The Facility can optimally accommodate up to 8 students at one time given space considerations, but can accommodate larger groups by dividing the students and rotating them through different stations/subjects during the allotted time. As a significant resource at a major, public land-grant University education is an important function of the Facility. Towards this end, the Facility provides tours, demonstrations, and lectures for any individual or group that would like to take advantage of this service. For example, the Facility offers tours with demonstrations to several classes at OSU, high school school students have done tours, and staff have done guest lectures in both college and high school classes. The staff is very flexible in order to meet the student's/class's needs. If the facility and staff can be of use to your education programs, then please contact us to discuss the possibilities.

    Tours, demonstrations, and lectures are FREE, but we do request a letter of thanks or acknowledgment that includes the name of the class or group, number of students, date and what activity the Facility performed. This is an important to the Facility in order to document our efforts.

    All other services are offered to OSU classes at a 40% discount of the list price.

  • Genotyping ( Service )

    The Facility can perform Genotyping by two methods: fragment analysis and high resolution melt analysis.

    The facility has a 3730 DNA Analyzer (Applied Biosystems, Inc.) that can analyze DNA fragments labeled with a fluorescent dye to determine the size of the fragment with a resolution of one base. With 48 capillaries the instrument can analyze up to 48 samples simultaneously as well as accommodate 96-, or 384-well plates. The 3730 DNA Analyzer has the ability to multiplex within one capillary by the use of 5 different fluorescent dyes, and/or differing fragment size. The facility can perform such techniques as allelic determination, amplified length polymorphism analysis (AFLP), microsatellite analysis (STR and SSR), and single nucleotide polymorphism analysis (SNapshot).

    The BioRad CFX96 real-time system can be used a specialized fluorometric based plate reader that can detect most dyes for applications such as high resolution melt analysis, single nucleotide polymorphism detection and measuring protein melting.

  • Microplate Reader ( Material analysis service )

    The facility has a SpectraFluor Plus (Tecan) that can measure the absorbance, fluorescence, and glow luminescence from samples in a 96-well or a 384-well plate.

    The plate reader has the ability to:

    measure from 230 to 700nm with the appropriate filter.
    incubate the plate from room temperature up to 42C.
    shake the plate in a linear or orbital manner
    perform timed measurements for kinetic analysis

    Currently the reader has the following band pass filters, but additional filters can be purchased if the need arises:

    Absorbance: 260, 280, 405, 340, 450, 492, 540, 620, 650nm.
    Excitation or Emission: 360, 430, 465, 485, 535, 590, 595, 635nm.

    The client brings in the samples/plates, and the staff will run the instrument at the client's direction. This is typically done while the client is present since results are immediate. For example, the concentration of 96 samples of PCR product can be measured by fluorescence in combination with fluorescent dye kit or various enzyme assays can be performed. So if you think this instrument can be of use to your research, then please contact the facility about its capabilities and how we can help.

  • Promoter Characterization ( Support service )

    Two traditional methods, DNA protection assay (DNA Footprint) and primer extension, that are used to determine promoter binding sites and transcription start sites respectively can be done at the Facility. Instead of using radioactivity and a porlyacrylamide gel the DNA is labeled with a fluorescent dye and the resulting fragments from the methods above can be analyzed with the automated capillary electrophoresis instrument at the Facility, i.e. a 3730 DNA Analyzer. In addition, non-radioactive gel shift assays are also commonly performed along with DNA Footprinting which the Facility also provides as a service.

  • Real-time PCR ( Material analysis service )

    The facility has a CFX96 Real-Time Detection System (BioRad) which can accurately quantitate PCR products in real time. The CFX96 system is very sensitive and can simultaneously measure up to 6 different PCR products in each of 96-wells. This system is adept at precisely measuring the concentration of specific RNAs, measuring gene copy number as well as perfoming other applicatons that require the measurement of specific DNA molecules. The CFX96 system can analyze all of the current detection chemistries, such as SYBR Green, Taqman, etc. In addition, the instrument can be used a specialized fluorometric based plate reader that can detect most dyes for applications such as high resolution melt analysis, single nucleotide polymorphism detection and measuring protein melting.

    The service includes the use of the CFX96 system and a file with the results. In addition the Facility can provide a copy of the CFX96 software at no cost to you. The Facility will provide the 96-well plate and optical film which is included in the per run cost. The customer will be responsible for providing all other consumables (e.g. primers, polymerase, nucleotides, etc.) and setting up the reactions in the plate.

  • Robotics, Liquid Handling ( Material analysis service )

    The Facility provides a robotic liquid handling service through the Beckman Biomek FX instrument which is more than a complex liquid handler, but also a biochemistry workstation. This robot has a 96-tip head for liquid handling and a set of gripper arms to move objects around its 20 position deck. Essentially it can do anything you can do with a pipette, but 96-tips at a time.





    In addition to places for tubes, tips, and fluid reservoirs the deck has:

    A vacuum manifold system for purifying and concentrating procedures
    A tip wash station to reduce costs
    Two areas for incubating plates at 4 - 75C
    A plate shaker.

    Sample List of Programs:

    Purify plasmid from 96 bacterial cultures by SeqPrep 96 HP kit.
    Copy bacterial libraries.
    Set up PCR reactions in eight 384-well plates simultaneously.
    Purify PCR products in 96- or 384-well plates.
    Analyze 96-PCR products or plasmids simultaneously by agarose electrophoresis.

    The robot is primarily for supporting the services at the facility, but this liquid handling platform can be used for functions other than those required by the Plant-Microbe Genomics Facility. So if you think it can be of use to your research, then please contact the facility about its capabilities as we have created many custom programs to support research at OSU.


Web Links:

Last updated: 2015-09-22T12:19:34.217-04:00

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