Genechip human gene 1.0 st microarray

To measure gene expression in archival FFPE tissue specimens, whole-transcriptome amplification using the WT-Ovation FFPE System V2 (NuGEN) was paired with microarray technologies using the GeneChip Human Gene 1.0 ST microarray (Affymetrix) as previously described.^{8 (link), 9 (link)} Expression profiles were processed by regressing out technical variables including mRNA concentration, block age, batch (96-well plate), percentage of probes above background, log-transformed average background signal, and median of the perfect match probes for each probe intensity of the raw data. The residuals were shifted to the original mean expression values and normalized using the robust multi-array average method.^{10 (link), 11 (link)} We mapped gene names to Affymetrix transcript cluster IDs using the NetAffx annotations as implemented in Bioconductor annotation package pd.hugene.1.0.st.v1, resulting in 20,254 unique gene names. Gene expression data are available through Gene Expression Omnibus (GSE79021).

Whole genome gene expression was measured in tumor and adjacent normal prostate using whole-transcriptome amplification (WT-Ovation FFPE system, v2, NuGEN) paired with microarray technologies (Affymetrix GeneChip HumanGene 1.0ST microarray).^{17 (link)} We processed the data, totaling 20,254 genes from tumor (n=229, of which n=30 were ever statin users) and normal adjacent (n=113, of which n=10 were ever statin users) tissues, as previously described.^{18 (link)} Data are available through the Gene Expression Omnibus (GSE79021).