The heterogeneous nature of most human organs and tissues represents a common challenge when analyzing specific structures or cells. Laser capture microdissection (LCM) enables isolation of pure cells from a mixed population of cells or tissue samples via usage of laser energy. Combined with high-throughput gene or protein techniques, compartment specific analysis elucidating the role of specialized cell types in physiological or pathophysiological activity can be performed. This chapter describes the crucial steps that have to be taken into consideration when designing and conducting a LCM project. Detailed protocols describing the workflow from project planning to high-throughput analysis of LCM material used in our laboratory are provided. Routinely occurring challenges and appropriate solutions, e.g., when working with fibrotic tissue are described.
Keywords: Laser capture microdissection; Microarray analyses; Preamplification; RNA extraction.