Fig. 6

Integration of single cell transcriptomes across the pregnancy cycle reveals intermediate states. a t-SNE and ternary plots of the integrated scRNA-seq profiles of epithelial cells isolated from adult (10 weeks), mid-pregnant (12.5 dP), late-pregnant (18.5 dP), lactating (8 day), and post-involution (3 weeks post-weaning) mammary glands from FVB/N mice (n = 4 mice for adult; n = 2 pooled mice for other stages). Cells are colored according to stage. The larger representation of alveolar cells in pregnancy and lactation reflects their abundance. b Same t-SNE plot as in a but colored by cell clusters. c Individual ternary plots showing lineage identity for each cell cluster from a. d Boxplots of signature expression scores for each of the 8 clusters in b by mammary epithelial or stromal subtype. e Heat map showing relative expression of the top 30 marker genes for each cluster in b. Color bars at the top of the heatmap represent the cluster and the stage. The arrow depicts “lineage-primed” cells in the basal compartment of lactating glands. f t-SNE plots (as in b) showing the expression of markers used for cell fractionation and definitive lineage markers and Mki67