ABSTRACT: The epididymis is comprised of multiple segments/compartments that, in addition to concentrating sperm and preventing their premature activation, play key roles in remodeling the protein, lipid, and RNA composition of maturing sperm. In order to understand the complex roles for the epididymis in reproductive biology, we generated a single cell atlas of gene expression from the murine epididymis and vas deferens using droplet-based (10X Chromium) single cell RNA-Seq. Following single-cell RNA-Seq, quality control, and removal of reads attributable to contaminating cell-free RNA we were able to profiled the expression of 16878 genes in 8,880 individual cells with an average of 3110 (median = 1965) unique molecular identifiers (UMIs) per cell from across the epididymis and the vas deferens. We recovered all the key cell types of the epididymal epithelium, including principal cells, clear cells, and basal cells, along with its associated support cells that include fibroblasts, smooth muscle, macrophages and other immune cells. Our data confirm and extend prior studies of segment-restricted gene expression programs, and reveal that these region-specific programs are largely driven by principal cells. In addition to the extensive region-specific specialization of principal cells, we find evidence for functionally-specialized subpopulations of stromal cells, and, most notably, two distinct populations of clear cells. Furthermore, we find several novel cell subpopulations, most notably including an Amylin-positive clear cell subtype, and predict intercellular signaling networks between the various cell types. Together, these data provide an atlas of cell composition across the epididymis, and a wealth of molecular hypotheses for future efforts in reproductive physiology.
