Abstract
BackgroundPresently, 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.ResultsArray 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.ConclusionWe conclude that of the platforms currently available and tested, the Affymetrix Porcine array is the most sensitive and reproducible microarray for swine genomic studies.
Highlights
Multiple options exist for conducting gene expression profiling studies in swine
Affymetrix Human and Porcine arrays were both highly correlated between technical replicates indicating high technical reproducibility
The lower correlation between replicates of the Affymetrix Human array is likely due to the greater percentage of inherently more variable non-hybridizing probes caused by sequence divergence mismatches
Summary
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. In spite of limited genomic information available, several platforms have been developed for gene expression profiling. There are two microarrays currently available for porcine gene expression studies: Affymetrix Porcine (24,123 probe sets), and a U.S Pig Genome Coordination Program glass spotted long oligonucleotide microarray (13,827 probes) [1,2]. A few groups have reported cross-species microarray hybridization onto Affymetrix Human arrays with mRNA from species such as dog, cattle, and swine [3,4], suggesting that the Affymetrix Human platform (54,676 probe sets) may be useful in porcine gene expression studies. There has been a single report of cross-species hybridization of porcine cDNA onto human nylon microarrays [5]
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