Comparison of sample-labeling techniques in DNA microarray experiments

Usage of DNA microarrays for gene expression analysis has become a common technique in many research laboratories and industry. Several target-labeling techniques have been devised to reduce the amount of RNA required for microarray experiments. In order to facilitate comparison and sharing of microarray data across the laboratories, it is crucial to determine the relative affects of these different sample-labeling techniques on the final results obtained from these experiments. We have compared two labeling methods designed for small RNA samples, an enzyme-based tyramide method (TSA) and a nucleic acid-based dendrimer method, to a more typical direct-labeling method that requires larger amounts of RNA. We observed comparable levels of reproducibility between replicate spots, with all the techniques. The dendrimer method resulted in a minimum number of spots (0.08%) that showed differential labeling due to a bias in the dyes used but resulted in highest background with only 71.4% of the spots measurable (above background) as compared to 93.3% for the TSA technique and 79.7% for the direct-labeling method. The results from differential labeling experiments showed that the dendrimer method performed better than the TSA method in detecting the same set of differentially expressed genes as observed with the direct method. Overall, our results show that the dendrimer method performs better than the TSA method. Differential labeling experiments using the TSA method show a non-linearity in the data at high intensities, leading to skewing of a portion of the data.