Abstract

Comparison of the performance of two-dye microarray platforms to characterize gene expression patterns

S. L. Rodriguez-Zas, R. E. Everts, B. R. Southey, J. K. Drackley, J. J. Loor, and H. A. Lewin. University of Illinois, Urbana.

ADSA/ASAS Joint Annual Meeting, Minneapolis, July 9-13, 2006

Microarray technology is a well-established tool to simultaneously measure the expression of thousands of mRNA sequences. The objectives of this study were to compare the performance of bovine cDNA and long-olignucleotide spotted microarray platforms, and to evaluate the impact of various sources of variation. The two platforms considered were a double spotted 7,872 element cDNA array (NCBI GEO GPL2864) and a double spotted 13,257 element long (70-mere) oligo array (NCBI GEO GPL2853). Two experiments using liver biopsies from multiparous cows at 14 DIM in a reference microarray design with reverse labeling were analyzed. The gene expression data were filtered, normalized and described using a mixed effects model including the effects of dye, treatment (ketosis and control), cow, and array. The estimates and significance probability values of 4,791 elements with one-to-one matches between platforms and the ability of selected probes to detect reported differential expression were evaluated. In the first experiment, the correlation between microarrays with reverse labeled samples ranged between 0.93 and 0.95 for the cDNA microarray and between 0.83 and 0.85 for the oligo microarray. The correlation between the log2 sample-to-reference ratio estimates between platforms ranged from 0.70 to 0.75 in both experiments and increased when elements with high differential expression were considered. The estimates of the log2 ratios within experimental treatment level from the oligo platform were more dispersed than the estimates from the cDNA platform, however the estimates of the log2 ratios across treatment levels studied were consistent across platforms. These results indicate that the oligo elements may be more sensitive to variations in gene expression intensity across the conditions studied. The results from selected oligo-probes were more consistent with reported values than the results from the corresponding cDNA-probes. Journal of Dairy Science, 89(Suppl. 1):in press.