Annual INBRE PI Meeting _______________________________________________ Dec. 7th, 2015 National Institutes of Health Lister Hill Auditorium Bethesda, MD Tim Hunter Manager, VGN Microarray Facility Vermont Genetics Network at the University of Vermont Director, Advanced Genome Technologies Core Best Practices in Core Facilities: Sustaining Crucial Resources

Advanced Genome Technologies Core Tim Hunter, Director VCC DNA Analysis Facility Services: Sanger DNA Sequencing: Fragment Analysis: –Genotyping, AFLP, T-RFLP, SNaPshot SNP detection Real-time qPCR: –Gene expression, Allelic Discrimination, PCR Arrays. Nucleic Acid extractions Methylation detection Molecular Imaging: -Phosphorimaging, Fluorescent detection, Fret, DNA and protein stain imaging, Chemiluminescence, Densitometry, and Photo documentation. BioTek Multi-plate Reader Experimental design consultation Troubleshooting Discounted pricing on reagents Common Equipment room with after hour access for qualified user VGN Microarray Facility Services: Experimental design consultation (jointly with Bioinformatics Group) Assistance in Nucleic Acid Extractions "LCM, Flow sorted, difficult tissues" RNA Quality/Quantity assessment Gene Expression Profiling DNA Mapping (SNP, LOH, CNV) Expression profiling using 3', Promoter, Exon and Gene Arrays Bacterial Identification using PhyloChip(TM) array Hypothesis testing: gene or pathway-based Support letters for grant applications; text for publication Discounted pricing on many consumables and reagents through core facility negotiations VCC-COM Massively Parallel Sequencing Facility Services: Experimental design consultation(jointly with bioinformatics group) Whole Genome sequencing mRNA (transcriptome) sequencing Methylation sequencing miRNA (ncRNA) sequencing ChIP sequencing Metagenomics Amplicon sequencing de novo sequencing Exome sequencing Targeted capture sequencing Discounted pricing on many consumables and reagents through core facility negotiations

VT INBRE: Vermont Genetics Network VT INBRE: PI: Judith Van Houten, PhD University of Vermont PC: Liz Dolci, PhD, Johnson State 7 – PUI 2 – Outreach PUI Community College of Vermont Landmark College

INBRE: Vermont Genetics Network Core Facilities Microarray Core  Established in 2002 (BRIN, Phase I, II, (III)) Bioinformatics Core  Established in 2002 (BRIN, Phase I,II, III) Proteomics Core  Established in 2005 (Phase I, II, III) Outreach Core  Established in 2003 (BRIN, Phase I, II) Professional Development and Education  Established in 2015 (Phase III)

“THE MOST IMPORTANT ASPECT OF A MULTI-USER CORE FACILITY IS THAT THE DATA GENERATED ARE ACCURATE AND USEFUL FOR THE GOALS OF THE RESEARCHERS” Core Facility Mantra: Lab Manager Magazine Oct./Nov vol.1, number 4

Best Practice #1 Develop an annual Business Plan: 1. Summary Plan: Where you are and where you want to be. 2. Describe your operation 3. Organizational Structure and Management 4. Services and Products: What do you offer and how 5. Identify your User Base: Capturing your market  Competitive Analysis 6. Impact/outcome metrics: Congruent with research mission of institute you serve 7. Marketing: Transparency of Core 8. Budgeting: financial needs, developing chargebacks

Best Practice #2 Budgeting: Develop two budgets Subsidized vs Fully Loaded WHY? Cognizant of true costs of delivering service Demonstrates Impact of INBRE funding to Institutes/Research Can serve as leverage

Best Practice #3 Make Your Core Visible  Present in Departmental Seminar Series  Lecture on Biotechnologies for undergrad and graduate level classes  Present at Local, Regional, and National Meetings NERIC, NISBRE, NERLSCD, ABRF, NESRS  Host your own Core Technology Seminar Series  Populate your core in the VGN Searchable Core Database

Best Practice #4 Engage your User Base  Annual Open House Daylong educational event  Annual Survey speakers, services, infrastructure, support  Workshops, Tutorials, Seminars  Oversight Committee  Open Forum

Best Practice #5 Acknowledging funding agency and core facility Solutions?  Post citation text on website/CMS (pdf)  Consult  Signed Agreement to comply  signatures

Best Practice #6 Inclusion of Core as a checkbox on SPA/OSP grant routing application  Grants submitted requiring research service support from Core  Grants submitted  Grants awarded

Best Practice #7 Collect Impact-Outcome Metrics throughout the year Resource Management : budget (surplus/deficit), new personnel, equipment, and new users, delivery of services Utilization: growth in user base, use by COBRE, INBRE, BPI faculty/staff /post docs, graduate, and undergraduate (#INBRE funded, #un-funded, Chargeback applied), # of experimental design consults Impact/Outcome: publications by users and grants awarded to users that included data generated in facility, Letters of Support, historical data. Education: involvement in graduate and undergraduate education, development of user workshops, student achievements Personnel Successes: Pubs and grants awarded to personnel; promotions, honors or awards, regional and national initiatives Personnel Development : attendance at workshops, technical courses, national meetings; institutional seminar series Communication of Services(Marketing): advertisement, website development and improvements, Regional Open Houses, national meetings Outreach: open house, pilot testing of new equipment or services, involvement in K-12 and undergraduate education, student internships

Best Practice #8 Inter-Core cooperation  Joint letters of support (NGS/Microarray and Bioinformatics)  Many projects transcend multiple cores to complete workflow in one core can impact results in another core Project required: 1.Coordination with two other cores (Microscopy Imaging and Bioinformatics) 2.Optimization of LCM processing to insure RNA is intact 3.Optimization of RNA extraction protocols 4.Identify and develop new approaches to perform microarray with low RNA input LCM- Epithelial Tissue Directly Slide-Post Staining Slide-Post LCM LCM -Stroma

“A successful core facility relies on a combination of knowledgeable staff that understands technological advances, have the ability to educate and inform users, and have a workable system of offering and delivering a service and meets the changing demands of its user base”

AGTC