Supplementary Figure 1: FACS strategies used for detection and sorting of EGFP⁺ mammary epithelial cell populations in single cell suspensions from Lgr6-CreERT2^+/− mammary glands at 5 weeks of age.

(a) FACS strategy applied to sort EGFP⁺ and EGFP⁻ mammary epithelial cells (quadrant I) from 5-6 week old mice for RNA sequencing analysis (b) Heat map of RNA-Seq transcriptome analysis from two experiments (Ex.1/Ex.2), showing all genes differentially expressed between Lgr6⁺ and Lgr6⁻ cells isolated from mammary glands of 5-6w-old Lgr6-CreERT2^+/− mice. Red indicates upregulated genes; blue indicates downregulated genes. (n = 6 mice for each of the 2 biological replicates). (c) FACS strategy for determining the distribution of EGFP⁺ cells over basal (lin⁻ CD29^hiCD24⁺) and luminal (lin⁻ CD29^loCD24⁺) MECs. The gate for EGFP⁺ cells was set using wildtype mice as fluorescence-minus-one (FMO) EGFP controls.