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

Juha K. Rantala (Corresponding Author), Rami Mäkelä, Anna-Riina Aaltola, Petra Laasola, John Mpindi, Matthias Nees, Petri Saviranta, Olli Kallioniemi (Corresponding Author)

Research output: Contribution to journalArticleScientificpeer-review

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Abstract

Background: 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.

Results: 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.

Conclusions: 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.
Original languageEnglish
JournalBMC Genomics
Volume12
Issue number162
DOIs
Publication statusPublished - 2011
MoE publication typeA1 Journal article-refereed

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Small Interfering RNA
Transfection
RNA Interference
Gene Knockdown Techniques
Prostatic Neoplasms
Survival
Growth
Research
Genes

Cite this

Rantala, J. K., Mäkelä, R., Aaltola, A-R., Laasola, P., Mpindi, J., Nees, M., ... Kallioniemi, O. (2011). A cell spot microarray method for production of high density siRNA transfection microarrays. BMC Genomics, 12(162). https://doi.org/10.1186/1471-2164-12-162
Rantala, Juha K. ; Mäkelä, Rami ; Aaltola, Anna-Riina ; Laasola, Petra ; Mpindi, John ; Nees, Matthias ; Saviranta, Petri ; Kallioniemi, Olli. / A cell spot microarray method for production of high density siRNA transfection microarrays. In: BMC Genomics. 2011 ; Vol. 12, No. 162.
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Rantala, JK, Mäkelä, R, Aaltola, A-R, Laasola, P, Mpindi, J, Nees, M, Saviranta, P & Kallioniemi, O 2011, 'A cell spot microarray method for production of high density siRNA transfection microarrays', BMC Genomics, vol. 12, no. 162. https://doi.org/10.1186/1471-2164-12-162

A cell spot microarray method for production of high density siRNA transfection microarrays. / Rantala, Juha K. (Corresponding Author); Mäkelä, Rami; Aaltola, Anna-Riina; Laasola, Petra; Mpindi, John; Nees, Matthias; Saviranta, Petri; Kallioniemi, Olli (Corresponding Author).

In: BMC Genomics, Vol. 12, No. 162, 2011.

Research output: Contribution to journalArticleScientificpeer-review

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AU - Rantala, Juha K.

AU - Mäkelä, Rami

AU - Aaltola, Anna-Riina

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AU - Mpindi, John

AU - Nees, Matthias

AU - Saviranta, Petri

AU - Kallioniemi, Olli

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AB - Background: 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.Results: 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.Conclusions: 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.

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