RNA-seq expression profiling of individual clones sorted from mouse mammary tumors

Breast tumors are characterized by inherent heterogeneity but the evolving cellular organization of breast tumors through progression remains poorly understood. Individual clones were tracked by combining mouse models of breast cancer with Confetti reporter strains. Expression profiling of individual clones sorted from tumors arising in K5- and Elf5-driven Pten/p53-deficient mice revealed distinct molecular signatures. K5-rtTA-IRES-GFP and ElF5-rtTA-IRES-GFP transgenic mice were crossed with TetO-cre (JAX) and R26R-Confetti reporter strains to generate triple genetically modified mice. The mice were treated with medroxyprogesterone acetate (MPA) and dimethylbenz(a)anthracene (DMBA) to induce carcinogenesis. Three K5-driven and five Elf5-driven mammary tumors were selected. Individual live cells from each tumor were FACS sorted by the four Confetti fluorescent markers (to select individual clones) and by CD24 expression (high or low). Cell subsets for the eight tumors, four fluorescent markers and positive or negative CD24 status were profiled by RNA-seq (38 samples in all). Expression was quantified by counting RNA-seq reads at the gene level and (separately) at the exon level.