Prostatic Stromal Cell Gene Expression. Homo sapiens

We generated prostatic stromal microarray expression data for functional validation of our LOH/AI hot-/cold-spots in stroma. Stromal cells from normal peripheral zone tissue and from tumors are grown in culture, and were analyed on gene expression platform. Overall design: Stromal cells cultured from normal peripheral zone tissues (F-PZ-64, F-PZ-79, F-PZ-82, F-PZ-102, F-PZ-105) and from tumors (F-CA-31, F-CA-39, F-CA-52, F-CA-67, F-CA-93) were established and grown as previously described in Peehl et al. (2000). Total RNAs were extracted from semi-confluent cells (passages 4-5) one day after feeding fresh medium using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions and treated with TURBO DNA-free kit (Ambion). Hybridizations were performed according to Illumina protocols by the Genomic Core, Lerner Research Institute, Cleveland Clinic. All samples were hybridized to the Illumina Sentrix Human-6_v3 Expression BeadChip (GPL6884) which contains 48,000 distinct oligonucleotide probes. Normalization is done using average normalization algorithm of BeadStudio Gene Expression Module v3.4 (Illumina).