Single cell expression data from ICM cells of mouse blastocysts

Transcriptional reactivation of the paternal X chromosome occurs in specific cells of the mouse blastocyst between E(mbryonic day)3.5 and E4.5 during pre- to peri-implantation development. While the trophectoderm (TE) and the primitive endoderm (PE) maintain Xist RNA expression and thereby imprinted silencing of genes on the Xp, the epiblast (EPI) cells within the inner cell mass (ICM) gradually downregulate Xist and undergo XCR. To identify differentially expressed genes with potential roles in the XCR process, we performed single-cell expression profiling of ICM cells of blastocysts prior (E3.5, EPI Xist+), during (E4.25, EPI Xist+/Xist-) and after (E4.5, EPI Xist-) XCR. Single cell cDNAs were then assigned to cell-type of origin using qPCR for lineage-specific marker genes (epiblast: Nanog+, PE: Gata6+, TE: Cdx2+). Cells were considered of male sex if they expressed the male marker Eif2s3y or female sex in absence of Eif2s3y and presence of Xist expression in PE cells of the same embryo. Furthermore, female E4.5 epiblast cDNAs were classified according to Xist expression as before (Xist+) or after (Xist-) downregulation during XCR. Single cell expression data of ICM cells of E3.5, E4.25 and E4.5 blastocysts were generated using the V1V3 method described in detail in [Kurimoto, K. et al., Nucleic acids research 34, e42 (2006); Kurimoto, K., Yabuta, Y., Ohinata, Y. and Saitou, M., Nature protocols 2, 739-752 (2007)].