Reactivation of the silenced X-chromosome during mouse germline development

X chromosome reactivation (XCR) occurs over a prolonged period during genome-wide reprogramming in female germ cells, initiating soon after primordial germ cell specification. The kinetics of XCRs remain poorly understood, as previous studies of XCR were based on a few genes. For a global appraisal of XCR dynamics, we performed single-cell RNA-seq on F1 female (XX(Xist?)) and male (XY) germ cells from E9.5 to E16.5 stages in development. Through the incorporation of interspecific crosses between C57B6J (B6) and Castaneus (CAST) parental mouse strains, containing a high number of informative single-nucleotide variants, we are able to distinguish gene expression from parental chromosomes in F1 embryos computationally.