ObjectiveTo investigate the difference of the gene expression profiles in dormant mouse embryos preserved by controlled slow freezing.MethodsThe differences between gene expression profiles of normal dormant mouse embryos and those preserved by controlled slow freezing were detected by Affymetrix Gene Chip detection. GO bioinformatics and pathway analysis were also applied for further understanding the potential changes of their signaling pathways. ResultsAfter the treatment by controlled slow freezing, a total of 228 genes were changed between these two groups. Among them, 50 genes were up-regulated, and other 178 ones were down-regulated. In addition, the signal pathway analysis revealed that the focal adhesion, ECM-receptor interaction, regulation of actin cytoskeleton, apoptosis, cell communication, ubiquitin-mediated proteolysis, glycerolphospholipid metabolism, small cell lung cancer signaling, TGF-beta signaling, and MAPK signaling pathways were significantly changed. ConclusionsThe results of our study indicate that controlled slow freezing leads to a series of potential changes of gene regulation and signaling pathways in dormant mouse embryos.