Open Access Research article

Detection of transcriptional difference of porcine imprinted genes using different microarray platforms

Shengdar Tsai13, Bashir Mir13, Amy C Martin13, Jose L Estrada13, Steve R Bischoff13, Wen-ping Hsieh4, Joseph P Cassady1, Bradley A Freking2, Dan J Nonneman2, Gary A Rohrer2 and Jorge A Piedrahita13*

Author Affiliations

1 Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA

2 USDA/ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA

3 Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC, USA

4 Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA

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BMC Genomics 2006, 7:328  doi:10.1186/1471-2164-7-328

Published: 28 December 2006

Abstract

Background

Presently, multiple options exist for conducting gene expression profiling studies in swine. In order to determine the performance of some of the existing microarrays, Affymetrix Porcine, Affymetrix Human U133+2.0, and the U.S. Pig Genome Coordination Program spotted glass oligonucleotide microarrays were compared for their reproducibility, coverage, platform independent and dependent sensitivity using fibroblast cell lines derived from control and parthenogenic porcine embryos.

Results

Array group correlations between technical replicates demonstrated comparable reproducibility in both Affymetrix arrays. Glass oligonucleotide arrays showed greater variability and, in addition, approximately 10% of probes had to be discarded due to slide printing defects. Probe level analysis of Affymetrix Human arrays revealed significant variability within probe sets due to the effects of cross-species hybridization. Affymetrix Porcine arrays identified the greatest number of differentially expressed genes amongst probes common to all arrays, a measure of platform sensitivity. Affymetrix Porcine 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.

Conclusion

We conclude that of the platforms currently available and tested, the Affymetrix Porcine array is the most sensitive and reproducible microarray for swine genomic studies.