Extended Data Fig. 9: Modelling the PFC–V1 split in the developing cortex.

a, b, UMAP projections of Z-scores of enrichment of PFC-specific peaks (a; n = 4,176) and V1-specific peaks (b; n = 21,030) in all PFC and V1 scATAC-seq cells (Fisher’s exact, two-sided, FDR < 0.05). c, Top enriched transcription factor motifs in V1-specific peak set as determined by HOMER (hypergeometric test, one-sided). d, UMAP projection of ChromVAR deviation scores of motif enrichment of MEF2C in all PFC and V1 scATAC-seq cells. e, UMAP projection of scRNA-seq data from organoids (n = 3) cultured in the presence of vitamin A, without the presence of vitamin A, and in the presence of DEAB. Cells coloured by cluster. f, Schematic depiction of classifier method used to assign area identity to organoid cells on the basis of defined area-specific gene modules. g, Bar plot depicting proportion of excitatory neurons from each treatment group classified as more PFC-like or more V1-like on the basis of calculation of module eigengene values for area-specific modules (see Methods). Asterisks indicate significant differences in proportions (DEAB: PFC, 1,160/2,622; V1, 1,462/2,622; NoVA: PFC, 563/1,556; V1, 993/1,556; VA: PFC, 1,831/2,976; V1, 1,145/2,976) (χ² test, one-sided, vitamin A versus no vitamin A: P = 3.209 × 10^–59; vitamin A versus DEAB: P = 2.79 × 10⁻³⁸). h, Violin plots depicting expression levels of SATB2, NR2F1, and NR2F2 for excitatory neurons from each treatment group. i, Heat map showing gene expression of differentially expressed genes between excitatory neurons cultured with and without vitamin A. j, Images of organoids cultured with and without vitamin A stained with DAPI and immunostained for NR2F1 and AUTS2. All images taken at 10× resolution. Representative images shown from n = 3 lines.