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Here, we describe a detailed protocol for the isolation of purified populations of viable spermatogenic cells derived from the non-human primate model organism Macaca fascicularis (cynomolgus). Using fluorescence-activated cell sorting (FACS), we describe methods to isolate spermatogonia and primary spermatocytes ranging across the sub-stages of meiosis prophase I. These cell populations can be used with a variety of downstream assays, including single-cell approaches such as RNA sequencing, chromatin immunoprecipitation, quantitative RT-P
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