Affymetrix HG-U133A gene expression profiles of 39 human breast cancer cell lines

Microarrays were used to detail the global programme of gene expression underlying breast cancer cell lines. We identified two main groups of luminal-type and basal-type breast cancer cell lines by unsupervised Pearson correlation of breast cancer cell lines and intrinsic subtyping. Supervised analysis on spindle versus non-spindle breast cancer cell lines identified a spindle cell signature of 1,144 genes identifying all spindle, basal-type, E-cadherin methylated breast cancer cell lines. Breast cancer cell lines were grown to optimal cell densities for RNA extraction and hybridization on Affymetrix microarrays.