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: 8167728
• 负责人: JEFFREY P. BOND
• 金额: $ 2.06万
• 依托单位: UNIVERSITY OF VERMONT & ST AGRIC COLLEGE
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-07-01 至 2011-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8167728
• 关键词: Antibody Formation; Bioinformatics; CD4 Positive T Lymphocytes; Centers of Research Excellence; Computer Retrieval of Information on Scientific Projects Database; Computer software; DNA Sequence; Data Storage and Retrieval; Development; Faculty; Funding; Genetic; Genetic Transcription; Grant; Informatics; Institution; Interleukin-6; Laboratories; Libraries; Manuscripts; Measurement; Mediating; Medicine; Organization administrative structures; Paper; Play; Preparation; Productivity; Publications; Reporting; Research; Research Personnel; Resources; Role; Services; Source; Staging; Systems Biology; Technology; United States National Institutes of Health; Vermont; Work; base; college; 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. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. 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.***

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 概述 * 请注意，下面提到的图表不会以这种格式复制。 请参阅随纸质副本发送的附件。* 本报告所述期间的核心B活动包括 +支持12名COBRE研究人员量化全基因组表达 +参与制定一项计划，为COBRE研究人员带来大规模并行（下一代）测序技术。 支持全基因组表达实验 利用 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名研究者（13项实验，189个微阵列）相关。涉及初步讨论或系统生物学软件的服务支持了另外3名研究者（表2）。 生产力 一个出版物来自早期的支持（Rincon和同事，“IL-6诱导抗体产生是由CD 4 + T细胞产生的IL-21间接介导的。“J Exp Med.2009 206：69-78），一份手稿正在修订以重新提交（Matrajt和同事，“Genome-wide expression reveals Toxoplamsa gondii bradyzoite differentiation mutants are also impaired relating to switching into a novel extracellular tachyzoite stage.“，PLoS One），三份手稿处于手稿准备阶段（2份来自Teuscher实验室，1份来自Budd实验室）。 新兴技术：大规模平行测序 Core B的Tim Hunter继续在将下一代测序引入UVM的努力中发挥核心作用。他参与开发了一项名为“佛蒙特州下一代DNA测序技术“（Nicholas Heintz，PI）的专项资金申请，该申请由UVM医学院院长办公室提交给参议员Leahy办公室。蒂姆·亨特和杰夫·邦德致力于将与大规模平行测序相关的核心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由Tim Hunter监督的涉及文库构建和测序的1FTE，以及生物信息学教员和1 FTE用于生物信息学分析。Vermont Genetics Network将提供与数据存储和预处理相关的服务（Jim Vincent和1名FTE TBN）以及1名用于下游分析的FTE。 图1.制定将大规模并行测序引入VCII的计划。三个组织单位，VCII（Tim Hunter和Jeff Bond），医学院（COM）和佛蒙特遗传学网络（VGN），正在合作提供实验室服务，信息学和统计服务，支持基于大规模平行测序的实验 * 表格和数字见附件：此处不转载。*