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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Reproduction Research » Research » Publications at this Location » Publication #186320


item Tsai, S
item Mir, B
item Martin, A
item Estrada, J
item Bischoff, S
item Cassady, J
item Weir, B
item Freking, Bradley - Brad
item Nonneman, Danny - Dan
item Rohrer, Gary
item Piedrahita, J

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.