DESCRIPTION


Project Objectives

  1. Establish a high-throughput workflow to enable a comprehensive cell-type expression atlas of rice.

  2. Build an expression profile atlas of rice cell types in juvenile and reproductive plants under standard growth conditions.

  3. Train students and postdocs in cell-capture, array hybridization and associated informatics.

  4. Educational outreach to primary and secondary students and the general public through exhibits and presentations at the Peabody Museum.

Summary of Strategy

PixCell IIe LCM Instrument
Arcturus Engineering

We are using a "microgenomic" approach to prepare an atlas of rice cell expression profiles, consisting of 135 individual datasets corresponding to cell types from all organs of normally developing rice. The atlas database can be enhanced in the future to include responses of specific cell types to environmental conditions, stresses, pathogens, metabolic & physiological conditions, etc. The workflow consists of the following:

  1. Cell isolation by laser-capture microdissection (LCM)

  2. Extraction and amplification of RNA

  3. Profiling on whole genome oligo arrays

  4. Public database that includes controlled vocabulary liilfor anatomical and deveopmental descriptors

Experimental Approaches

  1. The workflow consists of the harvest of diverse cell types by laser-capture microdissection (LCM), expression profiling of cells on the rice community microarrays being developed in another NSF project (PI: Pamela Ronald), development of a cell-type database, and prompt delivery of all data to TIGR for public access. Nelson is responsible for LCM and for RNA isolation, Deng for microarray profiling, and Zhao for database development and statistical analysis.

  2. The atlas center will provide to the community a basic expression database for the cell types of normally developing rice plants. The workflow and database will accommodate the acquisition of cell type data under other conditions such as pathogen infection, environmental stresses, physiological conditions, etc., in future projects. The collection of datasets will be ramped from year 1-4, for 135 datasets total.

  3. The training component benefits postdocs, graduate students and summer undergraduate interns recruited from under-represented groups.

  4. One public event per year at the Peabody Museum at Yale presents general information on rice and plant genomics, as well as results from this project.

Practical Applications of Research

A database of rice cell type expression data will be a resource for studies of virtually all aspects of rice biology, including growth, development, metabolism, physiology, pathology, stress responses, and so on. Since currently available genomic expression data has been based on samples of entire organs or tissues, it necessarily averages out the contributions of individual cell types. In contrast, a cell-type expression atlas will permit the detection of cell-specific expression patterns, networks of genes co-expressed in the same cell, potential interactions between different cell types, and other expression phenomena that require cellular resolution for analysis.