Fig. 1: Integration of the five scRNAseq data indicated a putative lineage trajectory in the mouse mammary epithelium.

a The overview of the integration process and the data. b The integrated data summarized in the 3D UMAP dimensionality and color-coded by the stages at the samplings. c The 2D UMAP projections of the integrated data color-coded by the clusters detected with the Louvain algorithm, the original studies, the mouse strains, and the stages at the samplings. d The cells from the prenatal glands and the expression of the selected marker genes were visualized in the UMAP dimensionality. Five thousand cells were sampled from the entire data for UMAP visualization. e The CytoTRACE scores are compared between C1 (n = 2404) and C2 (n = 2393), C3 (n = 2659) and C4 (n = 2429), and C5 (n = 828) and C6 (n = 2249) (biologically independent samples). Cliff’s delta values for the comaprisons of C1 and C3, C3 and C4, and C5 and C6 were 0.72 (CI: 0.70–0.74), 0.81 (CI: 0.79–0.82), and 0.53 (CI: 0.49–0.57), respectively. CI, confidence interval. The box-plot elements were defined as follows: center line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range; points, outliers. f The inferred trajectory of the mammary epithelial starting from the embryonic MaSCs and differentiating into the three distinct differentiated states (Basal, L-Alv, and L-Hor) through the corresponding progenitor clusters.