VERMONT IMMUNOBIOL/INFECTIOUS DIS CTR: MICROARRAY & BIOINFORMATIC ANALYSIS CORE

佛蒙特州免疫生物学/传染性盘 CTR：微阵列

• 批准号: 8360769
• 负责人: JEFFREY P. BOND
• 金额: $ 2.17万
• 依托单位: UNIVERSITY OF VERMONT & ST AGRIC COLLEGE
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-07-20 至 2012-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8360769
• 关键词: Antibody Formation; Bioinformatics; CD4 Positive T Lymphocytes; Centers of Research Excellence; Communicable Diseases; Computer software; DNA Sequence; Data Storage and Retrieval; Development; Faculty; Funding; Genetic; Genetic Transcription; Grant; Informatics; Interleukin-6; Laboratories; Libraries; Manuscripts; Measurement; Mediating; Medicine; National Center for Research Resources; Organization administrative structures; Paper; Play; Preparation; Principal Investigator; Productivity; Publications; Reporting; Research; Research Infrastructure; Research Personnel; Resources; Role; Services; Source; Staging; Systems Biology; Technology; United States National Institutes of Health; Vermont; Work; base; college; cost; design; extracellular; genome-wide; member; mutant; next generation; novel; research study; service utilization; statistical service

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. OVERVIEW ***Please note the Tables and Figures mentioned below would not reproduce in this format. Please see attachments sent with the paper copy.*** Core B activities during the reporting period included both +Support for 12 COBRE investigators quantifying genome-wide expression +Participation in development of a plan to bring massively parallel (next generation) sequencing technology to COBRE investigators. SUPPORT FOR GENOME-WIDE EXPRESSION EXPERIMENTS Utilization Services involving experiment design, genome-wide transcription measurements, or bioinformatics analysis were associated with 9 investigators (13 experiments, 189 microarrays). Services involving preliminary discussions or systems biology software supported an additional three investigators (Table 2). Productivity One publication resulted from earlier support (Rincon and coworkers, "The induction of antibody production by IL-6 is indirectly mediated by IL-21 produced by CD4+ T cells." J Exp Med. 2009 206:69-78), one manuscript is being revised for resubmission (Matrajt and coworkers, "Genome-wide expression reveals Toxoplamsa gondii bradyzoite differentiation mutants are also impaired with respect to switching into a novel extracellular tachyzoite stage.", PLoS One), and three manuscripts are at the stage of manuscript preparation (2 from the Teuscher laboratory and one from the Budd laboratory). EMERGING TECHNOLOGIES: Massively parallel sequencing Tim Hunter of Core B continues to play a central role in efforts to bring next generation sequencing to UVM. He participated in development of an application entitled "Next Generation DNA Sequencing Technology for Vermont " (Nicholas Heintz, PI) for earmark funding that was submitted to Senator Leahy's office from the Dean's Office in the UVM College of Medicine. Tim Hunter and Jeff Bond worked to integrate proposed Core B services related to massively parallel sequencing with services supported by the Dean's Office of the College of Medicine and the Vermont Genetics Network. Briefly (Figure 1), the earmark application proposes support for 1FTE involving library construction and sequencing, to be supervised by Tim Hunter, as well as a bioinformatics faculty member and 1 FTE for bioinformatics analysis. The Vermont Genetics Network will provide services related to data storage and preprocessing (Jim Vincent and 1 FTE TBN) as well as 1 FTE for downstream analysis. Figure 1. Development of a plan for bringing massively parallel sequencing to the VCII. Three organizational units, the VCII (Tim Hunter and Jeff Bond), the College of Medicine (COM), and the Vermont Genetics Network (VGN), are working together to provide laboratory services, informatics, and statistical services supporting experiments based on massively parallel sequencing ***Please see attachment for tables and figures: would not reproduce here.***

该子项目是利用资源的众多研究子项目之一 由 NIH/NCRR 资助的中心拨款提供。子项目的主要支持 并且子项目的首席研究员可能是由其他来源提供的， 包括其他 NIH 来源。 子项目可能列出的总成本 代表子项目使用的中心基础设施的估计数量， NCRR 赠款不直接向子项目或子项目工作人员提供资金。 概述 ***请注意，下面提到的表格和图形不会以这种格式复制。 请参阅随纸质副本发送的附件。*** 报告期内的核心 B 活动包括 +支持 12 位 COBRE 研究人员量化全基因组表达 +参与制定一项计划，为 COBRE 研究人员提供大规模并行（下一代）测序技术。 支持全基因组表达实验 利用率 涉及实验设计、全基因组转录测量或生物信息学分析的服务与 9 名研究人员相关（13 个实验，189 个微阵列）。涉及初步讨论或系统生物学软件的服务支持另外三名研究人员（表 2）。 生产率 一份出版物源自早期的支持（Rincon 和同事，“IL-6 产生抗体的诱导是由 CD4+ T 细胞产生的 IL-21 间接介导的。”J Exp Med. 2009 206:69-78），一份手稿是正在修改以重新提交（Matrajt 和同事，“全基因组表达表明弓形虫缓殖子分化突变体在转变为新的细胞外速殖子阶段。”，《公共科学图书馆一》），三份手稿正处于手稿准备阶段（两份来自 Teuscher 实验室，一份来自 Budd 实验室）。 新兴技术：大规模并行测序 Core B 的 Tim Hunter 在将下一代测序引入 UVM 的努力中继续发挥核心作用。他参与了题为“佛蒙特州下一代 DNA 测序技术”（Nicholas Heintz，PI）的专项资金申请的开发，该申请已从 UVM 医学院院长办公室提交给莱希参议员办公室。 Tim Hunter 和 Jeff Bond 致力于将拟议的与大规模并行测序相关的核心 B 服务与医学院院长办公室和佛蒙特州遗传学网络支持的服务整合起来。简而言之（图 1），专项拨款申请建议支持 1 个 FTE，涉及文库构建和测序，由 Tim Hunter 以及一名生物信息学教员和 1 个用于生物信息学分析的 FTE 监督。佛蒙特州遗传学网络将提供与数据存储和预处理相关的服务（Jim Vincent 和 1 个 FTE TBN）以及 1 个用于下游分析的 FTE。 图 1. 制定将大规模并行测序引入 VCII 的计划。 VCII（蒂姆·亨特和杰夫·邦德）、医学院 (COM) 和佛蒙特州遗传学网络 (VGN) 三个组织单位正在共同努力提供实验室服务、信息学和统计服务，支持基于大规模并行的实验测序 ***请参阅附件中的表格和图形：此处不会复制。***