Arabidopsis 2010: Development of a genome-scale cell type-specific gene expression map

拟南芥 2010：开发基因组规模的细胞类型特异性基因表达图谱

• 批准号: 0820842
• 负责人: Venugopala Gonehal
• 金额: $ 57.09万
• 依托单位: University of California-Riverside
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-02-01 至 2013-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0820842&HistoricalAwards=false
• 关键词: Arabidopsis; 2010; Development; genome; scale

Pattern formation in developmental fields is a dynamic process. It involves generation of specific cell types in a correct spatio-temporal sequence. Therefore, deciphering gene networks that underlie cell fate transitions requires new approaches aimed at assaying genome scale expression patterns of genes at a single cell type resolution. Shoot apical meristems (SAMs) of higher plants harbor a set of stem-cells and provide cells for the development of all the above-ground biomass of plants. Most of the important pattern formation events such as maintenance of stem-cell identity, specification and differentiation of leaf/flower primordia, and the temporal control of transition from vegetative to reproductive program are determined in the SAMs. Genetic analysis has revealed molecular and hormonal pathways involved in stem-cell maintenance, organ differentiation and flowering time. However, limited information is available as to how different pathways interact with each other to function as a network in specifying different cell types and their function. A major requirement for analyzing developmental gene networks is to determine gene expression profiles of different cell types, at a single cell type resolution. In this project, the PI and the co-PI will combine novel experimental approaches and bioinformatics analysis to generate a cell type-specific, genome-scale, expression map of the Arabidopsis shoot apex. The experimental methods of protoplasting SAMs cells, FACS-mediated sorting of fluorescently labeled protoplasts, fluorescently tagged transgenic seeds, the cell type specific microarray data, the relevant scripts and analysis tools such as PostgreSQL for the database backend, Python for its interface and R, JavaScript and Perl libraries for the online analysis and graphical tools will be available for download (www.CySAM.org). In addition, training will be provided for a post-doctoral fellow, and graduate and under-graduate students in designing new methods of isolation and separation of fluorescently labeled protoplasts and bioinformatic analysis of microarray data. The Center for Plant Cell Biology (CEPCEB) at UCR runs an NSF-sponsored REU program for undergraduates without research experience. Most students for this program are recruited from community colleges. The undergraduate students for this project will be recruited from the REU program and they will be exposed to state-of-the art cell isolation, genomic and bioinformatic technologies.

发展领域的格局形成是一个动态的过程。它涉及以正确的时空序列生成特定的细胞类型。因此，破译细胞命运转变的基因网络需要新的方法，旨在以单细胞类型分辨率测定基因的基因组规模表达模式。高等植物茎顶端分生组织（SAMs）含有一组干细胞，为植物地上部生物量的发育提供细胞。大多数重要的图案形成事件，如维持干细胞的身份，规格和分化的叶/花原基，和时间控制的过渡，从营养到生殖程序中确定的自组装膜。遗传分析揭示了参与干细胞维持、器官分化和开花时间的分子和激素途径。然而，有限的信息是如何不同的途径相互作用，作为一个网络，在指定不同的细胞类型和它们的功能。 分析发育基因网络的主要要求是以单个细胞类型分辨率确定不同细胞类型的基因表达谱。在这个项目中，PI和co-PI将联合收割机结合新的实验方法和生物信息学分析，以产生一个细胞类型特异性，基因组规模，拟南芥茎尖的表达图谱。SAMs细胞的原生质体化实验方法、荧光标记原生质体的FACS介导分选、荧光标记转基因种子、细胞类型特异性微阵列数据、相关脚本和分析工具，如用于数据库后端的PostgreSQL、用于其界面的Python以及用于在线分析和图形工具的R、JavaScript和Perl库，将可供下载（www.CySAM.org）。此外，还将为博士后研究员、研究生和本科生提供设计荧光标记原生质体分离和微阵列数据生物信息学分析新方法的培训。加州大学河滨分校的植物细胞生物学中心（CEPCEB）为没有研究经验的本科生开设了一个NSF赞助的REU项目。 这个项目的大部分学生都是从社区大学招募的。该项目的本科生将从REU计划中招募，他们将接触最先进的细胞分离，基因组和生物信息学技术。