Head and neck squamous cell carcinoma cell lines (HNSCC) compared with normal keratinocytes

Gene expression profiles of human HNSCC lines were compared with human normal keratinocytes by 24K cDNA microarray. The ten HNSCC analyzed are derived by the University of Michigan (UM-SCC), representing late stage SCC of different anatomic sites. Principle component analysis and hierarchical gene clustering classified ten cancer cell lines into two subsets, and associated each of the subsets with a distinctive p53 status. Keywords: Gene expression array-based Basal gene expression profiles were compared between ten cancer cell lines and normal keratinocytes from four individuals. RNAs were isolated from cancer cell lines and keratinocytes. After reverse transcription, these fluorescently-labeled cDNA were mixed with a labeled cDNA of reference RNA followed by hybridization on each array slide. Each array hybridization was repeated 2-4 times.