In this review, the history of single-cell transcriptomic analysis and their technical advantages over the conventional methods have been discussed. Recent advances in single-cell genomic techniques along with single-cell isolation methods, such as microfluidics and fluorescence-activated cell sorting, have helped elucidate the mechanisms underlying germ cell development and reproductive disorders in humans. Conventional genome-scale approaches cannot delineate the landscape of genomic, transcriptomic, and epigenomic diversity or heterogeneity in the differentiating germ cells of gonads. Hence, genome-scale analysis of germ cells at the single-cell level is challenging. Gonads contain a limited number of germ cells at various stages of differentiation. Germ cell formation is a complex process that is regulated by various mechanisms, including epigenetic regulation, germ cell-specific gene transcription, and meiosis. Mechanistic understanding of germ cell formation at a genome-scale level can aid in developing novel therapeutic strategies for infertility.
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