MCF-10A cells and their variants were all cultured as described on http://brugge.med.harvard.edu/. Other cell lines were cultured as described in the supplementary information. All assays on ECM detached cells were carried out 24 hours after plating on poly-HEMA coated plates unless otherwise noted. ATP assays were conducted using either the ATPlite assay (PerkinElmer, Waltham, MA), the ATP determination kit (Invitrogen, Carlsbad, CA), or the ATP/ADP Ratio Assay Kit (BioAssay Systems, Hayward, CA). Glucose uptake assays were performed using the Amplex Red Glucose Assay Kit (Invitrogen). ROS was measured using carboxy-H2DCF-DA in detached/attached cells and in 3D culture. To measure reduced glutathione, we used chloromethylcoumarin (CMAC, Invitrogen). FAO was measured by monitoring the release of 14CO2 after addition of 1-14C-Oleic Acid. 3D culture of mammary acini was completed according to the protocol at http://brugge.med.harvard.edu/. Native fluorescence of NAD(P)H was measured using two-photon microscopy. Soft agar assays were performed in the presence or absence of antioxidants and colony formation/size was determined using ImageJ.
Full methods and any associated references are available in the online version of the paper at www.nature.com/nature.