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Mink embryonic diapause occurs when embryos, at the blastocyst stage, enter a state of a reversible arrest in development and metabolism. Some ovarian factors are required because ovariectomy leads to prevention of implantation in mink. Mechanisms regulating this process, however, remain largely unknown. To explore ovarian modifications associated with emergence of embryonic diapause in mink, there was comparison of transcriptomes after embryonic activation to when there was embryonic diapause using RNA-sequencing. A library of 655 differentially expressed genes (DEGs) of all assembled 33,656 genes was generated. Among these, 558 genes were annotated with 106 genes being expressed to a greater extent in ovaries during embryonic diapause, whereas 452 genes were more abundantly expressed in ovaries after embryonic activation. The major categories of genes with differential transcript abundances include metabolic pathways, metabolism of tryptophan, tyrosine and vitamin B6, oxidoreductase activity, calcium signaling pathway, steroid biosynthesis and lysosome. The APOE and APOA1 hub genes identified through the protein-protein interaction (PPI) analysis have important functions in cholesterol transport and steroidogenesis. Transcript abundances associated with 39 genes were investigated using RT-qPCR procedures to confirm RNA-sequencing data. Of 29 mRNA transcripts, 26 were validated using RNA-sequencing, whereas three of ten indistinguishable genes determined using RNA-sequencing were confirmed. Most of these verified DEGs are involved in the prolactin signaling pathway, formation of functional corpora lutea, and steroid synthesis, suggesting these biological processes are implicated in embryonic reactivation. Overall, results provide new insights into ovarian signaling at the time of emergence of the blastocyst from diapause in mink. [ABSTRACT FROM AUTHOR]