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It directly affects the number of oocytes available to a female throughout her reproductive life. Premature depletion of primordial follicles contributes to the ovarian pathology primary ovarian insufficiency (POI). To delineate the developmental trajectory and regulatory mechanisms of oocytes during the process, we performed RNA\u2010seq on single germ cells from newborn (P0.5) ovaries. Three cell clusters were classified which corresponded to three cell states (germ cell cyst, cyst breakdown, and follicle) in the newborn ovary. By Monocle analysis, a uniform trajectory of oocyte development was built with a series of genes showed dynamic changes along the pseudo\u2010timeline. Gene Ontology term enrichment revealed a significant decrease in meiosis\u2010related genes and a dramatic increase in oocyte\u2010specific genes which marked the transition from a germ cell to a functional oocyte. We then established a network of regulons by using single\u2010cell regulatory network inference and clustering (SCENIC) algorithm and identified possible candidate transcription factors that may maintain transcription programs during follicle formation. Following functional studies further revealed the differential regulation of the identified regulon <jats:italic>Id2<\/jats:italic> and its family member <jats:italic>Id1<\/jats:italic>, on the establishment of primordial follicle pool by using siRNA knockdown and genetic modified mouse models. In summary, our study systematically reconstructed molecular cascades in oocytes and identified a series of genes and molecular pathways in follicle formation and development.<\/jats:p>","DOI":"10.1111\/acel.13424","type":"journal-article","created":{"date-parts":[[2021,6,26]],"date-time":"2021-06-26T22:26:13Z","timestamp":1624746373000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":34,"title":["Single\u2010cell RNA\u2010Seq reveals a highly coordinated transcriptional program in mouse germ cells during primordial follicle formation"],"prefix":"10.1111","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7019-6756","authenticated-orcid":false,"given":"Yuanlin","family":"He","sequence":"first","affiliation":[{"name":"State Key Laboratory of Reproductive Medicine Nanjing Medical University Nanjing China"},{"name":"Department of Epidemiology and Biostatistics International Joint Research Center on Environment and 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