a, Apoa1 expression in a subset of cells from time courses 1 and 2 (n = 48,515 cells). Fully reprogrammed iEPs are outlined in red (cluster 1). b, Density plot of the mean proportion of reprogrammed cells for groups of randomly selected cells (defined by cluster 1 occupancy; n = 59 groups, 10,259 cells). Randomized testing of 59 CellTagMEF/D3 clones (≥35 cells per clone, n = 10,259 cells) identifies iEP-enriched clones (n = 20 clones, 6,128 cells; P < 0.05) and iEP-depleted clones (n = 24 clones, 3,177 cells; P < 0.05). c, Clones spanning all time points were selected for further analysis. Trajectories showing connections between areas of highest clonal density across each day of reprogramming for iEP-depleted clones (left, n = 7 clones, 2,270 cells) and iEP-enriched clones (right, n = 7 clones, 1,037 cells). d, Pseudotemporal ordering of the time course 1 and 2 subset in a, with overlay of individual cells derived from iEP-enriched and iEP-depleted clones, defining reprogramming and dead-end trajectories (n = 14 clones, 3,307 cells). e, Proportions of clones occupying clusters 6 and 7 (reprogramming transition) or cluster 4 (dead-end transition) at reprogramming day 21 (r = −0.84, Pearson’s correlation; n = 44 clones, 9,305 cells). f, Lineage trees of related clones, with the proportion of each clone contributing to reprogramming or dead-end trajectories shown (n = 1,185 cells).