Fig. 1.

Protocol of a single-dye DNA-microarray assay. For microarray assay, tissues or cells are treated with a chemical A or the vehicle (DMSO, control). Total RNA is isolated and used for cDNA synthesis. Target cDNA (control and test samples) is labeled with the same fluorescent dye and used for hybridization with the probes on the microarray. The signal intensity of each spot is detected and quantified by a fluorescent scanner. For data processing, the signal intensity is averaged among duplicated spots, and the ratio of the mean signal intensity for the test sample to that for the control is then calculated for each gene. The ratios of signal intensity for all genes are normalized against the mean ratio for the marker genes (yellow spots). Normalized values are used for correlation and/or cluster analyses