Protocols: MMTV-PyMT organoids were seeded in BME and treated with 1 μg/mL doxycycline or left untreated. After 72 hours, organoids were harvested and dissociated into single cell suspensions using TrypLE (Life technologies). Cells were sorted in PBS on a BD FACSMelody™ Cell Sorter (BD Biosciences). DAPI was used to exclude dead cells. For ZEB1 WT MMTV-PyMT organoids, 40,000 GFP- cells were sorted, while for ZEB1 OE MMTV-PyMT organoids, 20,000 GFP- and 20,000 GFP+ cells were sorted and pooled. After sorting, single cells were resuspended in PBS + 0.04% BSA at a final concentration of 1000 cells/µL. Cells were loaded on a GemCode Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell Gel Bead-in-EMulsion (GEMs). Single-cell RNA-Seq libraries were prepared using GemCode Single-Cell 3ʹGel Bead and Library Kit (10x Genomics) according to the manufacturer's instructions.