Open Access Highly Accessed Methodology article

A cell spot microarray method for production of high density siRNA transfection microarrays

Juha K Rantala1*, Rami Mäkelä1, Anna-Riina Aaltola1, Petra Laasola1, John-Patrick Mpindi12, Matthias Nees1, Petri Saviranta1 and Olli Kallioniemi12*

Author Affiliations

1 Medical Biotechnology, VTT Technical Research Centre of Finland, 20521 Turku, Finland

2 Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014 Helsinki, Finland

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BMC Genomics 2011, 12:162  doi:10.1186/1471-2164-12-162

Published: 28 March 2011



High-throughput RNAi screening is widely applied in biological research, but remains expensive, infrastructure-intensive and conversion of many assays to HTS applications in microplate format is not feasible.


Here, we describe the optimization of a miniaturized cell spot microarray (CSMA) method, which facilitates utilization of the transfection microarray technique for disparate RNAi analyses. To promote rapid adaptation of the method, the concept has been tested with a panel of 92 adherent cell types, including primary human cells. We demonstrate the method in the systematic screening of 492 GPCR coding genes for impact on growth and survival of cultured human prostate cancer cells.


The CSMA method facilitates reproducible preparation of highly parallel cell microarrays for large-scale gene knockdown analyses. This will be critical towards expanding the cell based functional genetic screens to include more RNAi constructs, allow combinatorial RNAi analyses, multi-parametric phenotypic readouts or comparative analysis of many different cell types.