The protein kinase C (PKC) activator phorbol 12-myristate 13-acetate (PMA) induces transition of the epithelial MCF-7 cell line to a mesenchymal phenotype. A subset of the resulting mesenchymal cells has surface markers characteristics of a cancer stem cell (CSC) population. We profiled the transcriptome changes associated with the epithelial to mesenchymal transition and those that occurred in the CSC subset. Using a siRNA knockdown strategy, we examined the extent to which these changes were dependent on the PKC family member, PKC-¿. The importance of the cytoplasmic signaling role of this kinase is well established and in this study, we have shown by PKC-¿ ChIP-sequencing analysis that this kinase has a dual role with the ability to also associate with chromatin on a subset of PKC-¿ dependent genes. In the associated manuscript (Zafar et al., 2014 ) we presented evidence for the first time showing that this nuclear role of PKC-¿ is also important for gene induction and mesenchymal/CSC phenotype. Here we describe the analysis associated with the transcriptome and ChIP-seq data presented in Zafar et al. (2014)  and uploaded to NCBI Gene Expression Omnibus (. GSE53335).