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.***

该副本是利用众多研究子项目之一 由NIH/NCRR资助的中心赠款提供的资源。子弹和 调查员（PI）可能已经从其他NIH来源获得了主要资金， 因此可以在其他清晰的条目中代表。列出的机构是 对于中心，这不一定是调查员的机构。 概述 ***请注意，以下提到的表和数字不会以这种格式复制。 请参阅带有纸质副本的附件。*** 报告期内的核心B活动包括 +支持12个毛线研究人员量化全基因组表达的研究者 +参与制定计划，将大规模平行（下一代）测序技术带到鞋底研究人员。 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位研究人员相关（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了另外三名研究者（表2）。 生产率 一份出版物是由较早的支持（Rincon和同事）产生的，“ IL-6诱导抗体的产生是由CD4+ T细胞产生的IL-21间接介导的。对于切换到新型的细胞外旋转阶段，突变体也受到损害。 新兴技术：大规模平行测序 核心B的蒂姆·亨特（Tim Hunter）继续在将下一代测序带入UVM方面发挥核心作用。他参与了题为“佛蒙特州的下一代DNA测序技术”（尼古拉斯·海恩茨（Nicholas Heintz））的申请，该申请是从UVM医学院的迪恩（Dean）办公室提交给参议员Leahy's Office的指定资金。蒂姆·亨特（Tim Hunter）和杰夫·邦德（Jeff Bond）致力于将与大规模平行测序相关的拟议核心B服务与受到医学院院长办公室和佛蒙特州遗传学网络的支持的服务相结合。简而言之（图1），指定的申请提出了涉及图书馆构建和测序的1FTE的支持，由蒂姆·亨特（Tim Hunter）监督，以及生物信息学教职员工和1 FTE进行生物信息学分析。佛蒙特州遗传学网络将提供与数据存储和预处理（Jim Vincent和1 FTE TBN）以及1 FTE有关的服务，以进行下游分析。 图1。将大规模平行测序带到VCII的计划的制定。 VCII（Tim Hunter和Jeff Bond），医学院（COM）和Vermont Genetics Network（VGN）的三个组织部门正在共同努力，以提供基于非常平行的顺序的实验室服务，信息学和统计服务支持实验 ***请参阅表格和数字的附件：不会在这里复制。***