ShEEP Request for High-throughput Single Cell Genomics Instrumentation

ShEEP 请求高通量单细胞基因组学仪器

• 批准号: 9795153
• 负责人: Sandeep K Mallipattu
• 金额: --
• 依托单位: NORTHPORT VA MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-01-01 至 2019-09-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9795153
• 关键词: Award; Biological Process; Biopsy; Cell Line; Cells; Collaborations; Contract Services; DNA; DNA Sequence; Development; Disease; Disease Progression; Epigenetic Process; Equipment; Evolution; Fee-for-Service Plans; Functional disorder; Funding; Future; Gene Expression; Genetic Transcription; Genomics; Heart failure; High-Throughput Nucleotide Sequencing; Human Resources; Hypertension; Individual; Investigation; Kidney Diseases; Liquid substance; Location; Malignant Neoplasms; Medical center; Microfluidic Microchips; Microfluidics; Minor; Mission; Oncogenic; Pathogenicity; Population; Preparation; Process; Program Evaluation; RNA; Reaction; Research; Research Personnel; Research Support; Running; SNP genotyping; Sampling; Secondary to; Stress; System; Technical Expertise; Technology; Time; Tissue Sample; Training; Traumatic Brain Injury; Universities; Variant; Veterans; base; cDNA Expression; cost; design; digital; disease mechanisms study; epigenomics; high throughput analysis; insight; instrument; instrumentation; medical schools; next generation sequencing; single cell analysis; transcriptomics; tumor

In this Veterans Affairs ORD Shared Equipment Evaluation Program (ShEEP) application, we are requesting instrumentation for high throughput single-cell genomics (Fluidigm C1 Single-Cell Auto Prep System, 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 instrumentation will dramatically enhance Veterans Affairs (VA) and non-VA investigators to investigate mechanisms of disease progression at the level of single cells. Although dramatic advances have been made in the last decade in our ability to process and sequence DNA and RNA in bulk populations of cells, until recently our understanding of significant variations in genomic and transcriptomic information at the level of the single cell has been limited. For instance, major insights into fundamental biological processes such as normal development and tumor evolution secondary to oncogenic potential of single cells can only be garnered from a detailed 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 and characterization. Our Genomics Core is part of an ongoing collaboration to enhance the academic and administrative ties between the Northport Veterans Affairs Medical Center (NVAMC) and its affiliated Stony Brook University School of Medicine (SBUSM). This new instrumentation will be housed in NVAMC and this strategic location allows easy access to the instruments for both VA and SBUSM investigators. The location of this Core will encourage further collaboration between VA investigators at Northport and their University colleagues at Stony Brook. Technical support is available through the Genomics Core on a fee-for-service basis to support both VA researchers and their collaborators. In addition, we have assembled a team of experts for bioinfomatics support. Many of the VA investigators including Drs. Mallipattu, Lin, McKinnon, Rohatgi, Miller, Arvanian, Del Poeta, and Obeid, whose research are supported by Merit Review Awards, and would significantly benefit from the acquisition and utilization of this instrumentation for high throughput single-cell genomics. Trained personnel in the Core can operate the instrument and provide technical support and we have outlined a plan to purchase service contracts to maintain the instrument. In this ShEEP application for high-throughput single cell genomics instrumentation, we also describe in detail the specifics of the instrumentation, justification of need, demonstrate the technical expertise to support the usage of the equipment, descriptions of the major and minor users, and the organizational plan for the utilization of the instrumentation. The long-term impact of this single-cell analysis instrumentation is that it will enhance the impact and further our currently funded VA Merit Review Awards. In addition, results acquired from single-cell genomics will generate new hypothesis and provide new avenues for future investigations in diseases that are highly relevant to the VA mission.

在这个退伍军人事务部ORD共享设备评估计划（ShEEP）的应用程序，我们是 要求高通量单细胞基因组学仪器（Fluidigm C1单细胞自动制备 系统，BioMark，和Illumina NextSeq 550测序系统）来评估细胞特异性基因组， 与VA使命高度相关的疾病的表观遗传和转录组变异。该测量仪表 将大大提高退伍军人事务部（VA）和非VA调查人员调查的机制， 单细胞水平的疾病进展。虽然在过去的几年里已经取得了巨大的进步， 十年来，我们在大量细胞群中处理和测序DNA和RNA的能力，直到最近， 在单细胞水平上理解基因组和转录组信息的显著变化 是有限的。例如，对基本生物过程的主要见解，如正常的 发展和肿瘤演变继发于单细胞的致癌潜力，只能从一个 详细了解基因组，表观基因组和转录变异在单细胞水平。此外，本发明还提供了一种方法， 某些致病细胞是如此罕见，以至于单细胞方法对于它们的鉴定变得至关重要， 特征化 我们的基因组学核心是一个正在进行的合作，以提高学术和行政 北港退伍军人事务医疗中心（NVAMC）及其附属的斯托尼布鲁克大学之间的关系 医学院（SBUSM）。这种新的仪器将被安置在NVAMC和这个战略位置 允许VA和SBUSM调查人员轻松访问仪器。这个核心的位置 鼓励北港的退伍军人事务部调查人员与斯托尼大学的同事进一步合作 布鲁克技术支持可通过基因组核心在收费服务的基础上，以支持VA 研究人员及其合作者。此外，我们还组建了一个生物信息学专家小组， 支持.许多退伍军人事务部的调查人员，包括Mallipattu博士、Lin博士、McKinnon博士、Rohatgi博士、米勒博士、Arvanian博士、Del Poeta和Obeid，他们的研究得到了Merit Review Awards的支持，并将大大受益于 获得和利用这种仪器进行高通量单细胞基因组学。训练 核心的人员可以操作仪器并提供技术支持，我们已经制定了一个计划， 购买服务合同以维护仪器。 在用于高通量单细胞基因组学仪器的ShEEP应用中，我们还描述了 详细说明仪器的具体情况、需求的合理性，展示支持的技术专长 设备的使用情况、主要用户和次要用户的说明以及 仪器的使用。这种单细胞分析仪器的长期影响是， 提高影响力，并进一步我们目前资助的退伍军人管理局优秀评论奖。此外，取得的成果 将产生新的假设，并为未来的研究提供新的途径， 与退伍军人事务部使命高度相关的疾病。