Microarray Analysis Using a Limited Amount of Cells

Peterková, Martina; Koutná, I.; Tesařová, L.; Potěšilová, M.; Kozubek, M.; Hrabčáková, V.; Klabusay, M.; Doubek, M.; Mayer, J.

doi:10.14712/fb2009055020053

Folia Biologica > Archive > 2009, Vol. 55 > Issue 2 > Microarray Analysis Using a Limited…

Fol. Biol. 2009, 55, 53-60

https://doi.org/10.14712/fb2009055020053

Microarray Analysis Using a Limited Amount of Cells

Martina Peterková¹, I. Koutná¹, L. Tesařová¹, M. Potěšilová¹, M. Kozubek¹, V. Hrabčáková², M. Klabusay², M. Doubek², J. Mayer²

¹Masaryk University, Faculty of Informatics, Centre for Biomedical Image Analysis, Brno, Czech Republic
²Masaryk University, Faculty of Medicine and University Hospital Brno, Department of Internal Hematooncology, Brno, Czech Republic

Received August 2008
Accepted January 2009

cDNA microarray technology is widely used in various biological and medical disciplines to determine gene expression profiles. Unfortunately, this technology requires a large quantity of input RNA. Since there is an increasing need for more precise analyses of defined cell subpopulations with low cell counts, working protocols using a minimal number of input cells are required. Optimal RNA isolation and its accurate amplification are crucial to the success of these protocols. The HL-60 cell line was used in the search for a suitable protocol that can be used for clinical samples of CD34⁺ haematopoietic cells obtained from bone marrow. The goal was to discover the best method for isolating and amplifying RNA from a small number of cells. Our evaluation of various methods and kits available in the market revealed that the combination of RNAqueous™ Kit for RNA isolation and the SenseAmp Plus Kit for one-round RNA amplification produced the best results. This article presents a verified protocol describing a reliable and reproducible method for obtaining enough input RNA for microarray experiments when the number of cells is limited.