Enzymatic Methyl-seq (EM-seq) of doxycycline induced tumor and residual mouse primary mammary epithelial cells grown in 3D cell cultures against non-induced controls

This experiment investigates the genome wide DNA methylation landscape of residual breast cancer cells. Primary mammary epithelial cells taken from female mice with doxycycline-inducible hMyc- and Neu/Her2-oncogenes were grown in 3D organoid cultures. Upon the addition of doxycycline (200ng/mL) to the medium the expression of the oncogenes gets activated and the cells start uncontrolled proliferation resembling tumor growth. Tumor samples were taken after 5 days of oncogene induction. Subsequently, doxycycline was removed from the medium, which silences oncogene expression and results in rapid tumor regression. Residual samples reminiscent to the non-induced (normal) structures were taken after 7 days of de-induction (12 days overall). Non-induced structures were grown and sampled in parallel to the residual structures.