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

发展领域的模式形成是一个动态的过程。它包括在正确的时空序列中产生特定的细胞类型。因此，破译细胞命运转变背后的基因网络需要新的方法，旨在分析基因在单个细胞类型分辨率下的基因组水平表达模式。高等植物的茎尖分生组织（Shoot apical meristems, sam）包含一组干细胞，为植物地上生物量的发育提供细胞。大多数重要的模式形成事件，如干细胞身份的维持，叶/花原基的规范和分化，以及从营养程序向生殖程序过渡的时间控制，都是由sam决定的。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，关于不同的通路如何相互作用，作为一个网络来指定不同的细胞类型及其功能的信息有限。分析发育基因网络的一个主要要求是在单个细胞类型分辨率下确定不同细胞类型的基因表达谱。在这个项目中，PI和co-PI将结合新的实验方法和生物信息学分析来生成细胞类型特异性，基因组规模的拟南芥茎尖表达图谱。SAMs细胞原生质体的实验方法、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，如数据库后端PostgreSQL、接口Python以及用于在线分析和图形工具的R、JavaScript和Perl库，将提供下载（www.CySAM.org）。此外，将为一名博士后、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。UCR的植物细胞生物学中心（CEPCEB）为没有研究经验的本科生提供了一个由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。本项目的本科生将从REU项目中招募，他们将接触到最先进的细胞分离、基因组和生物信息技术。

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.