To determine the extent of the phenotypic differences between cancer cells in the same sample we performed single-cell transcript profiling on a panel of cell lines representing various subtypes of breast cancer including receptor positive ER + (MCF7), HER2 + (SKBR3) and TNBC (MDA-MB-231, HCC38) cell lines as well as freshly dissociated cells from a patient-derived xenograft (PDX) model of TNBC (HCI-002) using the 10 × Genomics Chromium platform (Fig. 1a). Here, ERBB2 is linked to breast cancer.