Multiple commercial microarrays for measuring genome-wide gene expression levels are
currently available, including oligonucleotide and cDNA, single- and two-channel formats.
This study reports on the results of gene expression measurements generated from identical
RNA preparations that were obtained using three commercially available microarray
platforms. RNA was collected from PANC-1 cells grown in serum-rich medium and at 24
h following the removal of serum. Three biological replicates were prepared for each
condition, and three experimental replicates were produced for the first biological
replicate. RNA was labeled and hybridized to microarrays from three major suppliers
according to manufacturers' protocols, and gene expression measurements were obtained
using each platform's standard software. For each platform, gene targets from a subset
of 2009 common genes were compared. Correlations in gene expression levels and comparisons
for significant gene expression changes in this subset were calculated, and showed
considerable divergence across the different platforms, suggesting the need for establishing
industrial manufacturing standards, and further independent and thorough validation
of the technology.