Fig. 6: Retrospective measurements link detachment of the Xi to cell cycle phase.
a, UMAP (n = 1,482 cells) based on Dam–LMNB1 levels in 100-kb-bins of the Xi coloured according to differentiation day. Streamlines on top of UMAP represent chromatin velocities inferred by the ratio of Dam–LMNB1 and LMNB1 in 100-kb-bins of the Xi, using scVelo29. b, Same UMAP as in a, but with cells coloured according to scVelo-inferred latent time, which is purely based on Dam–LMNB1/LMNB1 dynamics, not on the underlying UMAP. c, Single-cell heatmap showing log-transformed Dam–LMNB1 OE values on the entire inactivating X chromosome, with cells ordered along the inferred latent time shown in b. d, Scatter-plots showing the ratio of Dam–LMNB1 (x axis) and LMNB1 (y axis) in each cell for X chromosome bin 844 (marked in c). Length of arrows reflect the Dam–LMNB1/LMNB1 velocity of bin844 in that cell. Arrows are coloured according to differentiation day (top) or latent time (bottom). (e) Same UMAP as in a, coloured according to the ratio between Dam–LMNB1 and LMNB1. f, Same UMAP as in a, coloured according to the z-score normalized G1 cell cycle-phase enrichment, which is calculated with a k-nearest neighbours approach over the neighbourhood a cell belongs to (Methods). g, Scatter-plot of average Dam–LMNB1 (x axis) and LMNB1 (y axis) OE levels on the Xi. Each dot represents the Xi in one cell, coloured according to differentiation day. Distributions above and on the right show average density per day. Arrow is manually drawn based on directionality of cells over differentiation days. h, Same scatter-plot as in g, with points coloured according to the ratio between z-score-normalized G1 and G2 cell-cycle phase enrichment (Methods). Cell-cycle data are available in Supplementary Table 3.
