The Affymetrix GeneChip is a widely used gene expression profiling platform.
Given the complexity and multifactorial nature of the spread and accumulation of the infectious agent, we and others have used gene expression analysis platforms to identify signaling pathways that are altered during PrPSc accumulation and subsequent neurodegeneration.
To explore in which tissue or cell type our new proposed target genes are expressed, we used gene expression data from two different human microarray platforms, GNF1H and U95 Affymetrix chips information obtained from BioGPS (former SymAtlas) [ 48].
We used gene expression profiling using two different microarray platforms: one containing 25,000 oligonucleotide probes and one containing 18,000 cDNA probes.
For a more extensive comparison between the individual gene expression profiling platforms we used gene expression ratios between Wilms' tumor and Stratagene Universal reference RNA as determined by SAGE and Affymetrix GeneChips.
In order to clarify this question, some human, animal models and in vitro studies were undertaken using gene expression microarray platforms [ 17].
Since the various studies used different gene expression platforms, tumor selection criteria and isolation and labeling methods, it was impracticable to combine data from these studies with our data into one large dataset and perform a meta-analysis.
Further validation of these findings was obtained using a different gene expression platform with the nCounter NanoString technology.
However, although validation is essential, a predictive signature determined from a highly selected group of samples cannot possibly be expected to replicate the exact findings when applied to a different group of samples using a different gene expression platform.
While it would have been ideal to add a second validation method using an alternative gene expression platform (i.e. reverse transcriptase, polymerase chain reaction – qRT-PCR), we felt that the strength of our results made unnecessary the addition of an alternative validation method.
