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Title: MICROARRAY PLATFORM COMPARISON FOR PORCINE GENE EXPRESSION STUDIES

Author
item TSAI, S - NORTH CAROLINA STATE UNIV
item MIR, B - NORTH CAROLINA STATE UNIV
item MARTIN, A - NORTH CAROLINA STATE UNIV
item ESTRADA, J - NORTH CAROLINA STATE UNIV
item BISCHOFF, S - NORTH CAROLINA STATE UNIV
item CASSADY, J - NORTH CAROLINA STATE UNIV
item WEIR, B - NORTH CAROLINA STATE UNIV
item Freking, Bradley - Brad
item Nonneman, Danny - Dan
item Rohrer, Gary
item PIEDRAHITA, J - NORTH CAROLINA STATE UNIV

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 11/15/2005
Publication Date: 1/14/2006
Citation: Tsai, S., Mir, B., Martin, A., Estrada, J., Bischoff, S., Cassady, J., Weir, B., Freking, B.A., Nonneman, D.J., Rohrer, G.A., Piedrahita, J. 2006. Microarray platform comparison for porcine gene expression studies. Plant and Animal Genome Conference Proceedings. Poster #W241. p. 61.

Interpretive Summary:

Technical Abstract: In order to effectively conduct gene expression profiling in swine we examined the performance characteristics of three current microarray platforms. We compared Affymetrix Porcine (AP; 24,123 probesets), Affymetrix Human U133+2.0 (AH; 54,676 probesets), and a U.S. Pig Genome Coordination Program spotted glass oligonucleotide (GO; 13,827 probes) microarray platforms for their reproducibility, coverage, and platform independent and dependent sensitivity. RNA derived from fibroblasts of control or parthenogenetic porcine fetuses, was converted to cRNA for AH and AP, aRNA for GO and hybridized to each platform. The design consisted of triplicate biological and triplicate technical replications. Array group correlations between technical replicates showed the least variability in the AP array. GO arrays were comparable in variability to AH, after removing 13% of probes due to slide printing defects. Probe level analysis of AH arrays revealed significant variability within probe sets due to effects of cross-species hybridization. AP arrays identified the greatest number of differentially expressed genes amongst probes common to all arrays, a measure of platform sensitivity. AP arrays also identified the greatest number of differentially expressed known imprinted genes using all probes on each array, an ad hoc measure of realistic performance for this particular experiment (26 known imprinted genes, q < 0.05). We conclude that AP is currently the most sensitive and reproducible microarray platform for swine genomic studies. This project was supported by National Research Initiative Grant no. 2005-35604-15343 from the USDA Cooperative State Research, Education, and Extension Service to JP and BF.