Design, Construction, and Analysis of Cell Line Arrays and Tissue Microarrays for Gene Expression Analysis

  • Kathy GatelyEmail author
  • Keith Kerr
  • Ken O’Byrne
Part of the Methods in Molecular Biology book series (MIMB, volume 784)


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.

Key words

Cell line array Tissue microarray Immunohistochemistry Tissue arrayer Image acquisition system 



We would like to thank Elton Rexhepaj for providing the images in Fig. 2.


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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.Department of Clinical Medicine, Thoracic Oncology Research GroupInstitute of Molecular Medicine, Trinity Centre for Health SciencesDublinIreland
  2. 2.Department of PathologyAberdeen University Medical School & Aberdeen Royal InfirmaryForesterhillUK

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