Fig. 6: EpiTrace reveals the developmental history during human cortical gyrification.

a, UMAP projected cell evolution trajectory built with CellRank by using a hybrid kernel of EpiTrace, CytoTRACE and RNA velocity of an scMultiomic-seq dataset from a pcw21 human brain. EC, endothelial cell; IN, inhibitory GABAergic neuron; mGPC/OPC, medial ganglionic eminence progenitor/oligodendrocyte precursor cell; SP, subplate neuron. SPs and ECs are not shown in the figure due to space limitations. b, Trajectories built with only CytoTRACE (i) or RNA velocity (ii) resulted in unrealistic ‘sinks’ and ‘saddles’ on the map. In contrast, EpiTrace age (iii) provided a unidirectional reference of time to reveal that the ‘sink’ nIPC population is mitotically active to resolve the ‘nIPC stall’. c, Scatter plot of the differential gene expression estimate (−logP value, x axis) and differential TFBS-specific ChrAcc estimate (−logP value, y axis) in the GluN cells. Most significantly differential expressed transcription factors NR2F1 and TCF4 are highlighted in the figure. Differential expression was estimated by non-parametric Wilcoxon rank-sum test. d, UMAP of TFBS-specific ChrAcc of NR2F1. e, Expression of NR2F1 on UMAP. f, Expression of LMO3 on UMAP. g, EpiTrace age of cells belong to the LMO3⁺ population or NR2F1⁺ population. Sample numbers of biologically independent cells: 808 (LMO3⁺) and 1,198 (NR2F1⁺). P < 2.2 × 10⁻¹⁶ (Wilcoxon test, two-sided; the P value resulted in numerical underflow). h, CytoTRACE of cells belong to the LMO3⁺ population or NR2F1⁺ population. Sample numbers as in g. P = 0.017 (Wilcoxon test, two-sided). i, Mitotic clock (EpiTrace) and differentiation potential (CytoTRACE) of the same cell in scMultiomic-seq. The CytoTRACE score was reversed to show differentiation from left to right to facilitate comparison with EpiTrace. Sample numbers of biologically independent cells: n = 646 (RG); 341 (Cyc. Prog.); 2,348 (nIPC/GluN1); 1,546 (GluN2); 798 (GluN3); 459 (GluN4); 223 (GluN5); 190 (SP); 359 (mGPC/OPC); 301 (IN3); 780 (IN2); 959 (IN1); and 31 (EC/Peric.). j, Excitatory neuron phylogeny built with mitotic clock, showing that GluN4/GluN5 are likely direct, early-born progenies of RG, whereas GluN2/GluN3 are likely late-born, immature progenies of nIPC. k, Overall model of corticogenesis in the light of EpiTrace. Data source: Trevino et al.⁶⁵. For box plots, the upper and lower bounds of boxes show 25% and 75% percentiles of the data. The median of data is shown as the horizontal line in the box. The distribution minima and maxima, defined as farthest data point distanced ≤1.5 IQR from the box bounds, are shown by the whiskers. The violin plot shows the empirically estimated density distribution of data.