Temperature validation experiment for custom array production

Microarrays have evolved from low-density cDNA or oligonucleotide arrays to high-density platforms, for several study species even covering the complete transcriptome. At the same time, transcriptomics experiments have become more complex and multifactorial in nature, requiring many microarrays to assess multiple biologically relevant hypotheses. Scientists using this technology are therefore painfully aware of the high financial cost of a typical microarray experiment. Unfortunately, this often leads to either a suboptimal experimental design in an effort to reduce the cost by using fewer microarrays, or to abandoning microarray technology altogether. In this study, we argue that for many studies high-density full genome microarrays are in fact technical overkill. By selectively reducing full genome probe sets to a lower number of probes, it is possible to significantly reduce the total cost of a microarray experiment. The study consists of four microarray analyses: a cadmium probe selection experiment, a temperature probe selection experiment, a cadmium validation experiment and a cadmium validation experiment. Samples were hybridized in a simple loop design, in which every sample was labelled once with the red dye and once with the green dye. The hybridization design for the temperature validation experiment was (T26D4R2 > T34D4R1 > T26D4R3 > T34D4R2 > T26D4R2). Arrows (>) indicate individual microarrays; heads represent the green dye and tails represent the red dye. Sample names are of the form TaDbRc (temperature a in °C, day b, biological replicate c).