A comprehensive roadmap of spermatogenesis and testis niche from single-cell RNA-seq

Continuous sperm production is not necessary for the survival of the organism, but is essential to maintain a species. The process of spermatogenesis is comprised of three phases: mitotic proliferation, meiosis, and spermiogenesis. To illuminate germline intrinsic and extrinsic programs, we performed single-cell RNA sequencing on ~35K cells from the adult mouse testis. This analysis provides a comprehensive molecular atlas of the testis, identifying both known and novel cell types. We demonstrate for the first time the continuous nature of germ cell differentiation, provide molecular signatures and subtype-specific molecular markers, and identify several novel candidate regulators of spermatogenesis. Finally, we demonstrate in vivo using spatial mapping that germ and somatic cell molecular subtypes correspond to previously defined histological cell types residing at different stages of seminiferous epithelial cycle. Taken together, our results unveil the complexity of the testis, and provide a global, unbiased roadmap of the in vivo gametogenesis program. Overall design: Drop-seq of whole mouse testis and enriched populations. NOTE: As the initial submission of raw data only included partial run (extracted mouse cells) for some samples, all raw data for the following samples have been replaced to include the complete/original run for each sample (Feb 2019): GSM3069439, GSM3069440, GSM3069443-GSM3069448,GSM3069450, GSM3069451, GSM3069459-GSM3069463 All raw data for the 25 samples are paired-end, with 8 single-species samples + 17 mixed-species samples. For mixed-species samples, the major species is mouse, and the spike-in can be either human or monkey. The spike-in species were only used to confirm cells are not doublets by two-species mixing experiments, but not analyzed in processed data under GSE112393.