Quantitative assessment of DNA microarrays - Comparison with Northern blotanalyses

DNA microarray is a powerful technology that provides the expression profil e of thousands of genes. However, less attention has been paid to its quant itative aspect. In this study, we constructed a small-scale DNA microarray that contains 84 genes and characterized its quantitative aspect. Analyses with this microarray showed that 17 genes were induced, whereas 8 genes wer e suppressed at least twofold during the differentiation of mouse embryonic stem cells. When repeated with the same combination of fluorescent dyes fo r probe labeling, the microarray produced consistent data (correlation coef ficient = 0.991). In contrast, data were less consistent when repeated with the reverse combination of dyes (correlation coefficient = 0.945). The eff ect of dye combination was particularly evident in several genes. Total RNA (15 mug) and poly(A) RNA (0.5 mug) showed comparable sensitivity and produ ced essentially identical data (correlation coefficient = 0.983). The sensi tivity of the DNA microarrays was slightly inferior to that of Northern blo t analyses. In most genes, data obtained with the two methods were consiste nt. However, in 4 of 46 genes compared, DNA microarrays failed to detect th e expression changes that were revealed by Northern blot. These data demons trated that DNA microarrays provide quantitative data comparable to Norther n blot in general, but a few issues must be considered when analyzing data. (C) 2001 Academic Press.