GoKawiila, Upset plot showing intersections of regulons at central nervous system at each stage. b, Spatial visualization of the HMGA2 regulon activity (top) and expression (bottom) in the brain and spinal cord, and the color bar represents regulatory activity score (top) and scaled gene expression level (bottom). c, RNA ISH image of HMGA2 and DCX in the developing brain. The images are representative of 3 independent experiments. d,e, Bubbleplot showing the expression of cell marker genes for different neural cells (d) and RGCs subpopulations (e). f, Spatial mapping of different RGCs subpopulations. g, The shift in proportions of RGCs subpopulations over different developmental stages. h, Expression of HMGA2 in different neural cells. i, Heatmap shows the normalized expression of gene sets S1 (exhibiting an inverse expression gradient) and S2 (a concordant gradient) relative to HMGA2 expression in human Pall VZ, and the color bar represents scaled gene expression level. j, Profile plot shows the averaged HMGA2 ChIP-seq signals of gene sets S1 and S2 (top). Barplot shows the averaged HMGA2 ChIP-seq signals of gene sets S1 and S2 (bottom). Data are presented as mean ± SEM (n = 4 biologically independent experiments). Initially, ANOVA was conducted to assess overall differences, followed by Tukey’s multiple comparison test for multiple comparisons to determine specific pairwise differences between the gene sets. k, HMGA2 binding patterns were grouped into four clusters using k-means clustering (k = 4). Profile plot shows the averaged HMGA2 ChIP-seq signals of 4 clusters (top). Heatmap shows the HMGA2 ChIP-seq signals ranging from 3,000 bp upstream of the TSS to 3,000 bp downstream of the TES (bottom). l, Differences in gene expression for each cluster between neocortical NPCs of Hmga2−/− mice and those of control mice. Data are presented as box plots, with the boxes representing the median and upper and lower quartiles and the whiskers indicating the range. Statistical significance was assessed using Kruskal-Wallis test followed by Dunn’s post hoc test with Bonferroni correction for multiple comparisons. m, The expression of the rostrocaudal axis expression of the gene set cluster3 in mouse (E15.5 E1S3) Pall VZ were grouped into 3 Sets using k-means clustering (k = 3). Data are presented as heatmap, and the color bar represents scaled gene expression level. n, GO enrichment analysis of the 3 Sets. The p-value was calculated by the one-tailed hypergeometric test to assess the statistical significance of the enrichment. o, Left panel, heatmap showing the regulon modules grouped by Hotspot at sections CS18 E1S1. Right panel, spatial visualization of modules in the brain. p, Left panel, heatmap showing the regulon modules grouped by Hotspot at sections CS19 E1S1. Right panel, spatial visualization of modules in the brain. q, Gene regulatory networks of module CS19_M1. Selected target genes and TFs in the DDG2P were shown.
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