Fig. 1

Schematic of the mouse cell lines used to generate sci-Hi-C, sci-RNA-seq, and sci-ATAC-seq. A B6 x spret cross was used to generate Patski fibroblasts (top box), and 129 x cast crosses were used to generate mouse ESCs F123 (male), F121-6 (female), and ES_Tsix-stop (female) (lower box). Cells were collected during ESC differentiation to embryoid bodies at d0, d3, d7, and d11, followed by collection of neural precursor cells (NPCs). The XCI status is indicated in dark red. The B6 chrX is always the Xi in Patski cells. The male F123 line has a single Xa from 129. The cast or 129 chrX can be inactivated at random in differentiated F121-6, but due to a strong Xce allele, the 129 chrX is more often the Xi. In the cloned F121-6 NPC line, the 129 chrX is always the Xi. In ES_Tsix-stop cells in which XCI has occurred, the 129 chrX is always the Xi. Images of each culture are shown at right. Single cells were processed for sci-Hi-C, sci-RNA-seq, and sci-ATAC-seq as described in the text