Selection of candidate genes for further analysis. (A) Venn diagram summarizing expression of genes, as determined by RNA-Seq, targeted by shRNAs with FDR < 0.01 in freshly isolated MaSC/basal, LP and ML populations and MaSC/basal-derived mammosphere (Mammosphere) populations. (B) qRT-PCR profiling of two candidate regulators, Prox1 and Asap1, in primary epithelial subsets (n = 3; mean ± S.E.M). (C) Immunohistochemistry showing PROX1 and ASAP1 protein expression in mammary epithelial cells of 8-week-old virgin mice. (D) Representative FCM plots showing the relative abundance of MaSC/basal cells transduced with shControl-GFP, shProx1-GFP or shAsap1-GFP retrovirus and competitor cells transduced with control mCherry-expressing retrovirus at Day 2 and Day 7 in i3T3 cultures. (E) Histogram showing the change in the ratio of shRNA-GFP+: mCherry+ cells for each shRNA between 2 and 7 days of co-culture. Data from 3 independent experiments displayed as mean ± S.E.M. Statistical significance was calculated relative to shControl: shProx1, p ≤ 0.035; shAsap1, p ≤ 0.013.