title: Design, construction, and analysis of cell line arrays and tissue microarrays for gene expression analysis.
abstract: Cell line array (CMA) and tissue microarray (TMA) technologies are high-throughput methods for analysing both the abundance and distribution of gene expression in a panel of cell lines or multiple tissue specimens in an efficient and cost-effective manner. The process is based on Kononen's method of extracting a cylindrical core of paraffin-embedded donor tissue and inserting it into a recipient paraffin block. Donor tissue from surgically resected paraffin-embedded tissue blocks, frozen needle biopsies or cell line pellets can all be arrayed in the recipient block. The representative area of interest is identified and circled on a haematoxylin and eosin (H&E)-stained section of the donor block. Using a predesigned map showing a precise spacing pattern, a high density array of up to 1,000 cores of cell pellets and/or donor tissue can be embedded into the recipient block using a tissue arrayer from Beecher Instruments. Depending on the depth of the cell line/tissue removed from the donor block 100-300 consecutive sections can be cut from each CMA/TMA block. Sections can be stained for in situ detection of protein, DNA or RNA targets using immunohistochemistry (IHC), fluorescent in situ hybridisation (FISH) or mRNA in situ hybridisation (RNA-ISH), respectively. This chapter provides detailed methods for CMA/TMA design, construction and analysis with in-depth notes on all technical aspects including tips to deal with common pitfalls the user may encounter.
authors: Department of Clinical Medicine, Thoracic Oncology Research Group, Institute of Molecular Medicine, Trinity Centre for Health Sciences, Dublin, Ireland. KGately@stjames.ie
authors: Kathy
authors: K
authors: Gately
authors: Keith
authors: K
authors: Kerr
authors: Ken
authors: K
authors: O'Byrne
mesh_terms: D045744:Cell Line, Tumor; D004247:DNA / Q000032:analysis*; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D007150:Immunohistochemistry; D009369:Neoplasms / Q000235:genetics; D016612:Paraffin Embedding; D012333:RNA, Messenger / Q000032:analysis*; D012107:Research Design; D046888:Tissue Array Analysis / Q000379:methods*
chemical_list: D012333:RNA, Messenger; D004247:DNA