Understanding the control of gene expression is critical for our understanding of the relationship between genotype and phenotype. The need for reliable assessment of transcript abundance in biological samples has driven scientists to develop novel technologies such as DNA microarray and RNA-Seq to meet this demand. This review focuses on comparing the two most useful methods for whole transcriptome gene expression profiling. Microarrays are reliable and more cost effective than RNA-Seq for gene expression profiling in model organisms. RNA-Seq will eventually be used more routinely than microarray, but right now the techniques can be complementary to each other. Microarrays will not become obsolete but might be relegated to only a few uses. RNA-Seq clearly has a bright future in bioinformatic data collection.

Center for Molecular and Cognitive Neuroscience 1st Faculty of Medicine and Department of Biology and Medical Genetics 2nd Faculty of Medicine Charles University Prague Prague Czech Republic

Center for Molecular and Cognitive Neuroscience 1st Faculty of Medicine Charles University Prague Prague Czech Republic

Neuroscience Research Institute State University of New York College at Old Westbury Old Westbury USA

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