A Cost-effective Double-Stranded cDNA Synthesis for Plant Microarrays
DNA microarrays are two-dimensional arrangements of specific probes deposited on a substrate that have been widely used in gene expression analysis by measuring mRNA accumulation. The use of this type of microarrays involves the synthesis of cDNA, which has to be double stranded (ds) if the microarray probes are of the positive strand. We have used a melon custom-synthesized noncommercial NimbleGen microarray to evaluate a modification of the SMART™ (switching mechanism at the 5′ end of the RNA transcript) procedure of ds cDNA synthesis, which differs substantially in its economical cost relative to a widely recommended method based on the nick translation approach. The results suggested that both methods produce cDNA representative of the transcriptome to a similar extent, indicating that the alternative technique provides a cheaper method of ds cDNA synthesis for plant microarray gene expression assays when the RNA starting material is not limiting.