Abstract
BackgroundThe objective of this research was to investigate the reproducibility of cross-species microarray hybridisation. Comparisons between same- and cross-species hybridisations were also made. Nine hybridisations between a single pig skeletal muscle RNA sample and three human cDNA nylon microarrays were completed. Three replicate hybridisations of two different amounts of pig RNA, and of human skeletal muscle RNA were completed on three additional microarrays.ResultsReproducibility of microarray hybridisations of pig cDNA to human microarrays was high, as determined by Spearman and Pearson correlation coefficients and a Kappa statistic. Variability among replicate hybridisations was similar for human and pig data, indicating the reproducibility of results were not compromised in cross-species hybridisations. The concordance between data generated from hybridisations using pig and human skeletal muscle RNA was high, further supporting the use of human microarrays for the analysis of gene expression in the pig. No systematic effect of stripping and re-using nylon microarrays was found, and variability across microarrays was minimal.ConclusionThe majority of genes generated highly reproducible data in cross-species microarray hybridisations, although approximately 6% were identified as highly variable. Experimental designs that include at least three replicate hybridisations for each experimental treatment will enable the variability of individual genes to be considered appropriately. The use of cross-species microarray analysis looks promising. However, additional validation is needed to determine the specificity of cross-species hybridisations, and the validity of results.
Highlights
The objective of this research was to investigate the reproducibility of cross-species microarray hybridisation
These authors concluded that more reliable analyses of gene expression data are obtained by pooling data from multiple replicates, and recommended that at least three replicate hybridisations be completed for each experimental treatment
Gene expression data generated across replicate hybridisations was highly reproducible for the majority of genes on the microarrays
Summary
The objective of this research was to investigate the reproducibility of cross-species microarray hybridisation. Nine hybridisations between a single pig skeletal muscle RNA sample and three human cDNA nylon microarrays were completed. Three replicate hybridisations of two different amounts of pig RNA, and of human skeletal muscle RNA were completed on three additional microarrays. One approach for identifying novel genes associated with physiological pathways is to identify genes whose expression changes with differences in experimental treatment or phenotype. This approach has been implemented using several different techniques, including the use of cDNA microarrays to quantitate and evaluate the expression of thousands of genes simultaneously [1]. One alternative to developing species-specific microarrays may be to utilize (page number not for citation purposes)
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