Systems-wide RNAi analysis of different chr13 genes in colorectal cancer cell line (SW480). Homo sapiens

Expression profiles were generated for eight genes located on chromosome 13 following RNAi to enable the determination of gene specific LOF RNAi signatures in the colorectal cancer cell line SW480. Overall design: Triplicate transfections of SW480 cells were performed using two different siRNA duplexes corresponding to each gene target in 6-well plates using the same protocol scaled 30-fold. RNA was purified 72 hrs after transfection. RNA was also purified from negative control siRNA-transfected cells (AllStar siNegative (siNEG), Qiagen). Reduction in target mRNA levels was confirmed by real-time PCR prior to the array analysis.