10X Genomics scRNA-seq profiling of mammary gland cells from mice at different life stages

Background: Heterogeneity within the mouse mammary epithelium has been recently explored by single-cell RNA profiling. To further understand how cellular diversity changes during mammary development, we profiled single cells from different developmental stages including late embryogenesis, early postnatal, prepuberty, resting adult, mid-pregnancy, late-pregnancy, lactation and post-involution. We also compared the transcriptomes and chromatin accessibility of micro-dissected ducts versus terminal endbuds (TEBs) to help decipher the molecular properties of these specialized units that drive morphogenesis. Results: The single cell transcriptomes of 110,726 cells isolated from different stages were determined on the 10x Chromium platform and integrative analyses were performed to compare specific time-points. The mammary rudiment at E18.5 aligned more closely with the basal than the luminal lineage, while prepubertal epithelial cells at 2 weeks exhibited lineage segregation but to a less differentiated state than their adult counterparts. Integrated analysis of five stages spanning the pregnancy cycle revealed a novel alveolar progenitor that arises in late-pregnancy and stage-specific expression profiles. A continuum of states was uncovered along the basal-luminal progenitor cell axis following interrogation with >3,200 lineage-specific signature genes. Finally, exploration of micro-dissected TEBs and ducts showed that luminal cells within TEBs harbored intermediate expression profiles, and that ductal basal cells exhibited a higher level of accessible chromatin than their counterparts in TEBs. The data provides 18 biologically independent scRNA-seq profiles comprising a total of 149,371 cells supported by at least 500 sequence reads assigned to genes.