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Methods Mol Biol. 2013;959:235-45. doi: 10.1007/978-1-62703-221-6_16.

Gene expression analysis of shoot apical meristem cell types.

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Department of Botany and Plant Sciences, Center for Plant Cell Biology (CEPCEB), Institute of Integrative Genome Biology (IIGB), University of California, Riverside, CA, USA.


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 temporal control of the transition from vegetative to reproductive program are determined in 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. 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. Here we provide details of experimental methods involved in protoplasting of SAM cells, generating cell type-specific gene expression profiles, and analysis platforms for identifying and inferring gene networks.

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