Fig. 2: Timing of neurogenesis influences maturation competence.
From: Temporal control of progenitor competence shapes maturation in GABAergic neuron development in mice
a, UMAP plot showing FT datasets (n = 6,225 cells; n = 19 embryos) colored by injection and collection stage; injection at e12.5 and e16.5, scRNA-seq after 6 h or 96 h. b, Barplot showing relative cell number of postmitotic neuronal states in FTe12.5 + 6h, FTe16.5 + 6h and FTe12.5 + 96h. c, Violin plots showing the distribution of FT+ cells along the combined pseudotime trajectory, displayed for each condition; two-sided, unpaired Wilcoxon rank-sum test (****P < 0.0001, (P = 3.46 × 10−82, 2.87 × 10−255, 1.06 × 10−107), n = 2,000). The central point within the plot represents the median, hinges represent 25th and 75th percentile and whiskers show hinges ± 1.5 × interquartile range. d, Volcano plot displaying differential gene expression in postmitotic cells of FTe12.5+6h and FTe16.5+6h; |log2FC| > 1, Bonferroni-adjusted P < 0.05 using two-sided Wilcoxon rank-sum test. e, Heatmap showing average scaled expression of differential genes in FTe12.5+6h and FTe16.5+6h postmitotic cells; visualized in all FT+ conditions. f, UMAP plot showing scATAC-seq datasets (n = 23,647 cells; n = 19 embryos); FT injection at e12.5 and e16.5, followed by scATAC-seq after 6 h. g, Coverage plot displaying scATAC-seq and H3K4me1 signal intensity for peak categories. The x axis is relative position (basepairs) and the y axis shows average counts per million. h, Heatmap displaying the accessibility of CREs across pseudotime for FTe12.5 + 6h and FTe16.5 + 6h. Peaks are divided into ‘early’, ‘intermediate’ and ‘late’ based on accessibility profiles along pseudotime bins. Overlapping peaks are annotated in gray and unique peaks are annotated by stage-specific colors. Gray, overlapping motifs; blue, unique motifs. i, Volcano plot displaying −log10(P value) (y axis) and differential binding score (x axis) of TFs. P values were calculated using the subsampling procedure as proposed in ref. 38. Each dot represents a motif. j, Aggregate footprint profiles of NFIB in FTe12.5+6h and FTe16.5+6h. k, Coverage plot showing chromatin accessibility dynamics at NFIB footprint sites for FTe12.5+6h and FTe16.5+6h datasets.
