Extended Data Fig. 5: Gene regulatory network features of brain organoid development.

a, Numbers of chromatin access peaks and percentage of H3K27ac-marked peaks accessible at day 18–23 (>5% detection) intersecting with non-protein coding conserved regions (Cons.), candidate cis regulatory regions (CRE), or exons (left). b, Representative loci showing chromatin access (top) overlaying peak, CRE, conserved elements, and exon coordinates. c, Barplot showing the number of motifs used in GRN construction from two curated databases (JASPAR, CIS-BP), and motifs assigned through amino acid sequence similarity. d, Examples of 3 TFs with no motif annotation that were assigned motifs based on sequence similarity. e, Loci for two exemplary genes (FOXG1, WLS) showing average chromatin access signal tracks, accessible peaks, CREs, conserved elements, exons and H3K27ac CUT&Tag peaks. f, Scatter plot and histograms show explained variance (x) versus number of variables (y) of models for GRN construction. g, Violin plots show the distribution of peaks (left, n = 2535 target genes) and TFs per gene (middle, n = 2535 target genes), and number of genes per TF (right, n = 720 TFs). h, Representative loci showing average chromatin access signal tracks at different developmental branches overlaying inferred transcription factor binding sites within regulatory regions. i, UMAP representation of time course coloured by gene expression (log(transcript counts per 10k + 1)), gene module activity (module score calculated with Seurat) (rows), and regulatory module enrichment z-score (calculated with chromVAR) for representative TFs (columns). The range of values is indicated for each plot. j, Variation of module activity explained by branch, pseudotime, or branch and pseudotime (n = 720 TF modules). Box plot centre lines represent the median, boxes indicate 25%–75% interquantile range and whiskers 1.5 * interquantile range. k, Branch and pseudotime specific TF modules. Colours represent the branch with highest average module activity. TFs without experimentally validated motif are shown in grey.