New Technologies This NIH-funded regional program provides support for mechanistic, translational, and applied research that addresses health priorities in our northeast region Through the NNE-CTR (*), LCOM and OVPR support, we have enhanced our capabilities and provided new technologies to our shared resources MICROSCOPY IMAGING CENTER Spectral Imaging on Nikon A1R HD confocal upgrade (*) Spectral detector unit to image overlapping fluorescence dyes m Leica BOND RX Autostainer (*) Automated processing for IHC, ISH, RNAscope High-resolution/High-throughput microscope upgrade (*) Allows automated high-throughput imaging in 2D and 3D cells and organoids Indica Labs HALO image analysis platform (*) Quantitative tissue analysis in digital pathology; analyze morphological and multiplexed expression data on cell-by-cell basis across entire tissue section Benefits: Provides enhanced methodological choices for high-throughput, quantitative tissue analysis in oncology *image multiple antigens on a single tissue section, cultured cell, or organoid *fully automated staining protocols enhance reproducibility *automated fluorescence multidimensional confocal imaging on live samples For more information: http://med.uvm.edu/mic VERMONT INTEGRATIVE GENOMICS RESOURCE Illumina MiSeq Massively Parallel Sequencer (*) Sequencing for medium amplicon, cancer panels, targeted amplicons, ITS, 16s, and AmpliSeq panels Illumina MiniSeq Massively Parallel Sequencer Small amplicon, small genomes, 16s, 3’ QuantSeq RNA, microbial RNASeq, low-level shotgun sequencing, targeted amplicon, and AmpliSeq panels Oxford Nanopore GridIon X5 Long Read Sequencer Ultra Long DNA sequencing, direct RNAseq, full transcript RNASeq, epitranscriptomics (methylated RNA), large amplicon structural variants including Indels and rearrangements, full genome sequencing, scaffold and final genome assembly Up to 500kb single read lengths and up to 100 gigabases per run 10x Chromium Single Cell Genomics Platform (*) Sort and prepare single cell NGS sequencing libraries for RNASeq, ATACSeq, CNVs, Immune profiling, and long range sequencing using linked reads from heterogeneous cell populations BioRad QX200 digital droplet PCR (*) High precision DNA and RNA RTqPCR in digital format No standard curve required High PCR efficiency not required Used with SYBR green, Eva green, TaqMan assays, and standard AODs Applications for novel genomes and high precision molecular counting Benefits: Provides range of options for methodologies that maximize results and increase costeffectiveness * sequencing technologies that optimize acquisition of results based upon sample and analysis * single-cell RNAseq from heterogeneous population * RNA analysis from limited sample * enhanced reproducibility For more information: https://www.med.uvm.edu/uvmcancercenter/core-facilities/vigr FLOW CYTOMETRY AND CELL SORTING FACILITY Cytek Aurora flow cytometer: Equipped with lasers and 48 fluorescence channels, the Aurora is capable of detecting 23+ fluorophores Benefits: Provides a high-throughput, single-cell, quantitative assessment of the expression of 23+ parameters The innovative optical design of this instrument enables the use of a wide array of new fluorochrome combinations and greatly simplifies assay design For more information: http://www.med.uvm.edu/flowcytometry/home Technology Development Initiative (TDI) Award Guidelines Policies – TDI funds are intended to support research studies by NNE-CTR faculty aimed at the use of new methodologies/newly acquired technologies specifically for validating and optimizing the collection of preliminary data with intent to support extramural grant applications Applicants should clearly outline how the proposed research relates to current work in their laboratory and how the results will support one or more specific aims in an upcoming grant submission ***PLEASE READ GUIDELINES AND APPLICATION INSTRUCTIONS CAREFULLY *** All applicants must be registered members of the NNE-CTR Application for membership is available online:( https://collaborate.tuftsctsi.org/redcap/surveys/index.php?s=XYT7DDHE83) All full-time/salaried faculty members (0.75 FTE or greater) are eligible to request TDI funds All applications must be submitted to Jennifer Smith, Administrative Coordinator NNE-CTR, (Jennifer.smith@med.uvm.edu) as a single PDF file by noon October 11, 2019 Applications are subject to review In all cases, major consideration is given to: 1) the extent to which the proposed studies, if successfully completed, will enhance the investigator's competitiveness for extramural funding; 2) the ability of the proposed studies to strengthen the research activity and productivity of NNE-CTR faculty utilizing the Shared Resources of VIGR, MIC, and FCCS Applicants are encouraged to consult with the Directors of the Shared Resources to optimize the utilization of the new technologies Submission of a progress report is mandatory at the end of the funding period (1 year) This report must include a) a brief discussion of the results of the proposed study including an assessment of the new technologies, and b) a summary of specific aims arising from the data generated Application Checklist Cover PAGE Itemized Budget Body of Application- 3-page maximum o Background-premise o Approach o Anticipated results o Future plans Biosketch APPLICATION Instructions COVER PAGE: Title of application, $ requested, departmental approval (required if matching funds) ITEMIZED BUDGET PAGE BODY OF APPLICATION: The proposal should not exceed pages, which addresses each of the items listed below (A to C) The format, including type size, is to follow the standard NIH PHS grant (PHS-SF424) That is, “type should be 10-12 points (approximately 1/8” in height for capital letters) If constant spacing is used, there should be no more than 15 cpi, whereas proportional spacing should average no more than 15 cpi Finally, there must be no more than lines of text within a vertical inch.” Leave 1/2” margins A Specific Aim(s) and Hypothesis (