Fig. 6

Cell cycle analysis along pseudotime highlights a delay in differentiation associated with cell cycle arrest in aged condition. a Repartition (in percentage) of the cell cycle phases (estimated with cyclone) in young and aged HSPCs. b Repartition (in percentage) of the cell cycle phases (estimated with cyclone) in LTHSCs, STHSCs, MPP2 and MPP3 in young and aged conditions. For a and b, * indicates a significant dependence between cell cycle phase and age repartitions (p value < 0.05 Pearson’s chi-squared test). c Left panel, differentiation trajectory of HSPCs colored in accordance to their score for previously published quiescence and proliferation signatures. Right panel, comparison of the scores for the quiescence and proliferation signatures between young and aged HSPCs in pseudotime. d Density plot of young (orange) and aged (purple) cells along pseudotime for the T (left), NeuMast (middle), and MkEr (right) fates. Black and red dashed lines mark respectively p and pMye bifurcation points. e Division rate along pseudotime for young (orange) and aged (purple) HSPCs for the T (left), NeuMast (middle), and MkEr (right) fates. On x-axis, pseudotime was cut into 50 bins and a division rate is calculated for each bin, by dividing the number of young (resp. aged) cells assigned to G2M phase by the total number of young (resp. aged) cells of the bin. Black and red stretched lines mark p and pMye pseudotime bifurcation point respectively. f Stacked plot of predicted cell types along pseudotime cut into 50 bins for young (upper part of the plots) and aged (lower part of the plots), for the L (left), NeuMast (middle) and MkEr (right) fates. Black and red stretched lines mark p and pMye bifurcation point pseudotime respectively. g Smoothed gene expression along pseudotime of selected markers for young (upper panel) and aged (lower panel) HSPCs. Points represent cells, which are colored according to their belonging to the 5 different states (1 gray, 2 yellow, 3 green, 4 orange and 5 blue). The y-axis is in log scale. * indicates significant differences in gene expression between young and aged cells (p value < 0.05) and star color indicates the state where the difference is found