This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. VGN Lead Institution Highlights Purchased Mass Spectrometer for Proteomics Facility -Thermo-Finnigan LTQ 31000 LTQ Linear Quadrupole Ion Trap -Shimadzu CBM 20A Prominence Series HPLC system with autosampler and two pumps -Thermo-Finnigan - Bioworks 3.2 Software upgrade - Software upgrade for workstations working with new LTQ Mass Spec. Purchased computer equipment for the Vermont Advanced Computing Center -DataTrend Technologies - IBM 1350 Linux Cluster - Computer equpment for the Vermont Advanced Computing Center (VACC) Graduate Student Assistantships 6 Awards made for Project Year 1 Graduate Student Assistantship Competition complete for Project Year 2 (7 Awards made) UVM DNA Microarray Facility: Activities/Highlights Services Offered: -Consultation on experimental design in collaboration with the Bioinformatics Core Facility -Gene Expression Profiling -target preparation -gene expression, SNP, or mapping -eukaryotic and prokaryotic -single and double amplification -Nugen based target preps for low RNA targets, i.e., LCM -Hybridization and scanning -Mapping target preparation -RNA Integrity assessment -Nucleic Acid quantitation -RNA extraction assistance and training -SOP s established for all services offered Scientific or technical changes: -Incorporated ability to offer 500K mapping chips -Optimized target preparation protocol for FFPE samples for 500K mapping chips -upgraded to GS 3000 scanner allowing usage of higher density arrays including custom chips and new evolution genechips developed by Affymetrix -upgraded to GS450 Fluidics Station for full automation of Genechip washing and staining procedures -upgraded operating system from MAS v5 to GCOS (genechip operating system -Optimized methods and developed protocols to recover intact RNA from LCM -Developed joint letter of support for grant submissions with the Bioinformatic Core -purchased new gradient thermal cycler Professional Development: Staff attended and participated at the following meetings: -Tim Hunter: Association of Biomolecular Resource Facilities, Feb., 2006, Long Beach, CA -Tim Hunter and Scott Tighe: Affymetrix User meeting, May, 2006, San Francisco, CA Facility Promotion: -Hosted Open House May 26, 2005. Over 125 attendees -Provided Workshop on sample handling and new capabilities of GS 3000 scanner, May, 2005 -Hosted technology seminar: DNA Array Evolution-Whole Genome Analysis, Custom SNPs and Beyond March, 2005, Carl Raimond, AffymetrixGenotyping Devolopment Manager -Open House for Facility planned for May 2006 Facility Presentations: Invited Speaker: -Tim Hunter, Association of Biomolecular Resource Facilities, Feb.,2005, Savannah, GA, Validation of Microarray Data via Real-Time Quantitative PCR . -Tim Hunter, Association of Biomolecular Research Facilities, Feb., 2006, Long Beach, CA, Development and Optimization of a Multiplexed Real-Time Quantitative PCR Assay -Tim Hunter, University of Vermont Pharmacology Seminar Series, April, 2005, UVM DNA and Microarray Facilities: What We Can Do For You -Tim Hunter, University of Vermont OB/GYN Research Seminar Series, Feb., 2006, Tools and Technologies in the Modern Laboratory Meeting presentations (Poster): -Scott Tighe, Vermont Cancer Center Symposium, Oct., 2005, Burlington, VT, Strategies for Generating Microarray Data from LCM Derived Breast Tissue . Utilization: -Experimental design consultations with 16 investigators -Completion of 15 microarray projects (117 GeneChips) -Performed 99 RNA assessments: 31 PicoChips and 86 NanoChips It should be noted that a test chip was required for each target preparation until 2005
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