show Abstracthide AbstractEarly stem cell differentiation programmes are tightly controlled by coordinated pre- and post-transcriptional regulatory networks. In this study, we investigate and characterise miRNA networks responsible for the post-translational gene regulation in early differentiation in both female and male mouse embryonic stem cells. We obtained miRNA-Seq and RNA-Seq profiles of male and female cells from day 0 (D0; 2i) to days 4, 10, 20 and 30. Interestingly, we observed a significant difference in gene expression profiles between females and males, both in terms of identity of regulated genes and of temporal characteristics. Similarly, we observed differences between miRNA species playing significant regulatory roles in female and male cells. Overall design: mESC mRNA profiles during differentiation were generated by deep sequencing using Illumina.