Single Cell RNA Sequencing of Mouse Mammary Epithelial Cells

The mammary epithelial cell (MEC) system is a bi-layered ductal epithelial network consisting of luminal and basal cells, maintained by a lineage of stem and progenitor cell populations. Here, we used integrated single-cell transcriptomics and chromatin accessibility analysis to reconstruct the cell types of the mouse MEC system and their underlying gene regulatory features in an unbiased manner. We define differentiation states within the secretory type of luminal cells, which can be defined as a continuous spectrum of progenitor and mature secretory cells. By integrating single-cell transcriptomics and chromatin accessibility landscapes, we identified cis- and trans-regulatory elements that are differentially activated in the specific epithelial cell types and our newly defined luminal differentiation states. Our work provides an unprecedented resource to reveal cis/trans regulatory elements associated with MEC identity and differentiation that will serve as a valuable reference to determine how the chromatin accessibility landscape changes during breast cancer. Overall design: Library generation for three 10x Genomics v2 chemistry was performed following the Chromium Single Cell 3' Reagents Kits v2 User Guide: CG00052 Rev B. Libraries were sequenced on the Illumina HiSeq4000 platform targeting approximately 50,000 reads per cells.