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Microarray Outreach

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Microarray Outreach

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The Microarray Outreach Project of the Vermont Genetics Network was made possible through a supplement to the VGN grant funded by the NIH / NIGMS. A Microarray Outreach Team was assembled in early fall of 2003. The team developed a hands-on microarray laboratory module using the Affymetrix microarray platform to take to undergraduate schools in Vermont.

Current Team Members:

 
  • Tabitha Finch, Outreach Core Director
  • Heather Driscoll VGN Bioinformatics Faculty

GOAL:

The goal of the VGN Microarray Outreach project is to expose undergraduates in the state of Vermont to microarray technology using hands-on laboratory experiences. During our first visit to each BPI we provided teaching materials, laboratory materials and equipment for colleges within the state to run the module. The undergraduate students learn about this cutting edge technology and gain new skills that will help them with their future scientific careers.

OVERVIEW:

In this module, students learn how gene expression in yeast is changed after exposure to dimethyl sulfoxide (DMSO), a common environmental contaminant and solvent. Control yeast are exposed to water and treated yeast are exposed to 10% DMSO for 2 hours. RNA is then harvested and prepared for use on Affymetrix® yeast microarray chips. Prepared cRNA is taken back to the UVM Microarray Core Facility and hybridized to the yeast chips. The data are processed using the most recent probeset signal intensity algorithms including RMA and GCRM. The primary software utilized in visualizing gene expression differences is Genesifter®. Students are then taken through basic microarray data analysis procedures to generate lists of genes which are up or down regulated upon treatment with DMSO.

Integration and Module Adaptation

The beta test of the module was run at the University of Vermont in the fall of 2003 and was subsequently delivered to all Baccalaureate Partner Institutions between 2004-2006 (St. Michael's College, Middlebury College, Johnson State College, Norwich University, and Castleton University). Microarray Outreach was also to non-baccalaureate partner institutes; including, Green Mountain College in the fall of 2005, Lyndon State College in the fall 2006,  and to Marlboro College in the spring of 2007.

A second experimental protocol was developed inducing oxidative stress in the fission yeast Schizosaccharomyces pombe. This experimental protocol was beta-tested in the Biology Department at UVM in the Spring of 2007 and was delivered at Green Mountain College and Castleton University.

One of the goals of Microarray Outreach is the integration of this technology into the science curriculum at colleges throughout the state. We are achieving this goal with subsequent deliveries at several colleges; including, Johnson State College in the Spring of 2006; St. Michael's College and Middlebury College in the Spring of 2007; Norwich University and Green Mountain College in the fall of 2007; and Johnson State College, Castleton University, and Marlboro College in the Spring of 2008.

In the 2009/2010 academic year we had a record number of Microarray deliveries; including, Norwich University and Green Mountain College in the fall; Johnson State College, Lyndon State College, and Marlboro College in the Spring; and a collaboration with Bates College in Maine. The module was taught at Norwich University, Castleton University, Lyndon State College, and Johnson State College in 2011 and 2012. We are currently working with two faculty members at Green Mountain College to incorporate new research into the course.

One of our focuses has been adapting this module to meet the research needs of our different faculty partners and increasing the interest of many students in research efforts at their colleges. Efforts to adapt the microarray experiment include and further research include:

MATERIALS:

Manual:
The Yeast-DMSO Microarray Laboratory Manual can be downloaded as a PDF or DOC file.
Click HERE (PDF) to download.
Click HERE (DOC) to download.

Presentations:

Appendix Material:

  • Background
    • General Biology Review for DNA and RNA as well as gene and protein structure. Click HERE.
    • Amplified RNA synthesized from limited quantities of heterogeneous cDNA" PNAS USA (1990) - FREE PDF (PMID: 1689846) 
    • Tighe, S., Hunter, T., Reed, P., Murray, J. Microarray Analysis for Saccharomyces cerevisiae. J. Vis. Exp. (50), e2585, DOI: 10.3791/2585 (2011). View Here (Video Article)
  • Bioinformatics
    • "Dimethyl sulfoxide exposure facilitates phospholipid biosynthesis and cellular membrane proliferation in yeast cells" Journal of Biological Chemistry (2003) - FREE PDF (PMID: 12771156)
    • "Microarray analyses of the metabolic responses of Saccharomyces cerevisiae to organic solvent dimethyl sulfoxide" J Ind Microbiol Biotechnol (2003) - may require subscription (PMID: 12545388)
    • "Genomic expression programs in the response of yeast cells to environmental changes." Gasch AP , Spellman PT , Kao CM , Carmel-Harel O , Eisen MB , Storz G , Botstein D , Brown PO . Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5428, USA Mol Biol Cell. 2000 Dec;11(12):4241-57. (PMID: 11102521)

Other Experiments

  • Laboratory Manuals / Other Materials
    • The S. Pombe-Oxidative stress Microarray laboratory manual can be downloaded as a PDF or DOC file.
    • The Yeast-Oxidative stress microarray laboratory manual can be downloaded as a PDF or DOC file.
    • Click HERE (PDF) to download ( manual 2010).
    • Click HERE (DOC) to download (manual 2010). If you use this document to edit the manual for your own purposes please save as a pdf for your students to print out. This prevents formatting problems in printing.
    • The Yeast-water from mine tailings JSC 2012 microarray laboratory manual can be downloaded as a PDF or DOC file.
      • Click HERE (PDF) to download ( manual 2012).
        Click HERE (DOC) to download (manual 2012). If you use this document to edit the manual for your own purposes please save as a pdf for your students to print out. This prevents formatting problems in printing
    • The Arabidopsis lyrata - cold tolerance Microarray laboratory manual can be downloaded as a PDF or DOC file.
      • Click to download HERE (PDF) ( manual 2011).
      • Click to download HERE (DOC) (manual 2011). If you use this document to edit the manual for your own purposes please save as a pdf for your students to print out. This prevents formatting problems in printing.
        • PowerPoint Lecture Slides
    • Other specific powerpoint Lectures

Links to RNA Extraction protocol's:

Links to Web Resources on Microarrays:

 

Questions about the module? E-mail Tabitha.Finch@uvm.edu

Contact Information:

Vermont Genetics Network
University of Vermont
120A Marsh Life Science Building
Burlington, VT 05405-0086
(802) 656-9119
(802) 656-2914 - FAX
vgn@uvm.edu

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vgnwebstaff@list.uvm.edu

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