Vermont Genetics Network Microarray Programs use Pellet Paint® Co-Precipitant

An important mission for the Vermont Genetics Network (VGN) is to identify needs and develop facilities for biomedical research at the University of Vermont (UVM, Universitas Viridis Montis, Latin for “University of the Green Mountains”). Additional network goals are to: (1) assist UVM faculty researchers by providing set-up funding and graduate student support, (2) assist the Baccalaureate Partner Institutions (BPIs: Castleton and Johnson State Colleges, Middlebury College, Norwich University, and Saint Michael’s College) with student and faculty research support, (3) provide outreach programs to introduce modern biomedical research tools to undergraduate students throughout the Vermont higher education community. VGN opened the UVM DNA Microarray Core Facility in November 2002 in collaboration with the Vermont Cancer Center and the College of Medicine. The goal of the core facility is to provide microarray technology support services for prokaryotic and eukaryotic research conducted at the UVM and its BPIs.

DNA Microarray Core Facility

The DNA Microarray Facility’s expert staff, manager Timothy Hunter and Scott Tighe, consult with researchers on experimental design and perform array-based experiments for gene expression. The facility provides a variety of RNA expression-profiling services, from quality testing of RNA before microarray hybridization to primary data analysis and access to bioinformatics tools for further analysis. Tim and Scott use and recommend Pellet Paint® Co-Precipitant to precipitate cDNA synthesized from sample mRNA, in preparation for in vitro transcription of target cRNA. Target cRNA is then analyzed with an Affymetrix GeneChip® probe microarray.

For more information, visit:

http://www.med.uvm.edu/uvmcancercenter/core-facilities/genome-technologies/microarray

Pellet Paint Co-Precipitant

Pellet Paint Co-Precipitant is a visible, fluorescent dye-labeled carrier formulated for use in alcohol precipitation of nucleic acids (McCormick 1996a,b). The 2-min precipitation requires no low temperature incubation or prolonged centrifugation. Both RNA and DNA are efficiently precipitated from even dilute solutions (2 ng/ml) and the vivid pink color of the pellet can be easily followed during wash steps to prevent losses during handling. Pellet Paint Co-Precipitant does not interfere with many molecular biology procedures, including PCR, sequencing, restriction digests, ligation, transformation of E. coli, transcription, translation, cDNA synthesis, or RNase protection assays. When using Pellet Paint Co-Precipitant, nucleic acid concentrations can be determined by UV absorbance using the ratio listed on the tube label and the user protocol directions. The Pellet Paint fluorophore does interfere with rhodamine-labeled primers and terminators and may interfere with other methods based on rhodamine detection; for these applications, Pellet Paint NF Co-Precipitant, a non-fluorescent carrier, is available.

VGN Microarray Outreach

In addition to their work at the Microarray Core Facility, Tim and Scott are members of the VGN Microarray Outreach team, which developed a hands-on microarray laboratory module to use at undergraduate schools in Vermont. The Microarray Outreach program, directed by Dr. Christopher Allen and coordinated by Dr. Janet Murray, provides all necessary teaching and laboratory materials and equipment for schools to run the module. Lab manual instructions include using Pellet Paint® Co-Precipitant in the cDNA precipitation step and show an image of the pink pellet to provide an easy reference for students. An AVI video demonstrating how to clean the cDNA pellet can also be downloaded from the Microarray Outreach webpage.

Conclusion

Pellet Paint Co-Precipitant facilitates the precipitation of nucleic acids and pellet handling without interfering with most downstream techniques. We thank Timothy Hunter and Scott Tighe for their use of Pellet Paint Co-Precipitant and for sharing information about their work with us.

Materials

     
Related Links