• Mallipattu, Sandeep (PI)

Project Details


In this Veterans Affairs ORD Shared Equipment Evaluation Program (ShEEP) application, we arerequesting instrumentation for high throughput single-cell genomics (Fluidigm C1 Single-Cell Auto PrepSystem, BioMark, and Illumina NextSeq 550 Sequencing System) to evaluate cell-specific genomic,epigenetic, and transcriptomic variations in diseases of high relevance to the VA mission. This instrumentationwill dramatically enhance Veterans Affairs (VA) and non-VA investigators to investigate mechanisms ofdisease progression at the level of single cells. Although dramatic advances have been made in the lastdecade in our ability to process and sequence DNA and RNA in bulk populations of cells, until recently ourunderstanding of significant variations in genomic and transcriptomic information at the level of the single cellhas been limited. For instance, major insights into fundamental biological processes such as normaldevelopment and tumor evolution secondary to oncogenic potential of single cells can only be garnered from adetailed understanding of genomic, epigenomic, and transcriptional variation at the single-cell level. In addition,certain pathogenic cells are so rare that single-cell approaches become essential to their identification andcharacterization. Our Genomics Core is part of an ongoing collaboration to enhance the academic and administrativeties between the Northport Veterans Affairs Medical Center (NVAMC) and its affiliated Stony Brook UniversitySchool of Medicine (SBUSM). This new instrumentation will be housed in NVAMC and this strategic locationallows easy access to the instruments for both VA and SBUSM investigators. The location of this Core willencourage further collaboration between VA investigators at Northport and their University colleagues at StonyBrook. Technical support is available through the Genomics Core on a fee-for-service basis to support both VAresearchers and their collaborators. In addition, we have assembled a team of experts for bioinfomaticssupport. Many of the VA investigators including Drs. Mallipattu, Lin, McKinnon, Rohatgi, Miller, Arvanian, DelPoeta, and Obeid, whose research are supported by Merit Review Awards, and would significantly benefit fromthe acquisition and utilization of this instrumentation for high throughput single-cell genomics. Trainedpersonnel in the Core can operate the instrument and provide technical support and we have outlined a plan topurchase service contracts to maintain the instrument. In this ShEEP application for high-throughput single cell genomics instrumentation, we also describe indetail the specifics of the instrumentation, justification of need, demonstrate the technical expertise to supportthe usage of the equipment, descriptions of the major and minor users, and the organizational plan for theutilization of the instrumentation. The long-term impact of this single-cell analysis instrumentation is that it willenhance the impact and further our currently funded VA Merit Review Awards. In addition, results acquiredfrom single-cell genomics will generate new hypothesis and provide new avenues for future investigations indiseases that are highly relevant to the VA mission.

Effective start/end date1/01/1930/09/19


  • U.S. Department of Veterans Affairs


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