Extended Data Fig. 5: Further characterization of epigenome dynamics in human cortical organoids.

(A-B) Heatmaps displaying accessibility levels. (C) Scatterplot depicting CpG methylation levels of individual GpC peaks. Peaks that significantly (FDR ≤ 0.05) lose (RGC DMR; n = 663) or gain methylation (IPC DMR; n = 66) are colored. Grey dots indicate peaks that do not change significantly CpG methylation (n = 65551). (D) Boxplots displaying gene expression fold changes for genes associated with either RGC or IPC DARs. Statistical significance was calculated using an unpaired two-sided Wilcoxon rank-sum test (n = 3391 and 5445 linked genes for RGC and IPC respectively). (E) Boxplots depicting contact strength (Hi-C score) of pairs of distal RGC DARs and their associated gene based on highest Hi-C score in RGC (n = 6358 pairs). Scatterplot colored by density represents the same individual RGC DAR – gene pairs and their Hi-C score. Statistical significance was calculated using a two-sided Wilcoxon rank-sum test. (F) Same as (E) but for IPC DAR and IPCs (n = 13845 pairs). (G) Average GpC accessibility levels of RGC and IPC at GpC peaks centered on the NEUROG2 motif (n = 10662, 10 bp bins). (H) Scatter plot showing the enrichment of TF motifs within NPC DMR. Red and blue dots indicate significantly (p < 0.01; abs(logFC) ≥ 0.25) enriched or depleted motifs, respectively. (I) Average methylation levels of RGC or IPC at GpC peaks centered on the NEUROG2 motif (n = 10662) (20 bp bin size, coverage 10x). (J) Scatterplot colored by density depicting changes of methylation and GpC accessibility between RGC and IPC for individual GpC peaks containing the NEUROG2 motif (n = 10662). Spearman’s correlation is indicated in the left top corner. (K) Average CpG methylation levels of RGC or IPC across RGC DARs with (right; n = 3459) or without (left; n = 3020) LHX2 motif (20 bp bins). (L) Aggregated contact enrichment for RGC and IPC between RGC DARs without LHX2 motifs. (M) Same as (K) but for IPC DARs with (n = 9,116) and without (n = 3721) NEUROG2 motif. (N) Same as (L) but for IPC DARs without NEUROG2 motif. (O) Genomic tracks depicting the Nfia locus in the developing mouse cortex. All boxplots display the median (line), 25th and 75th percentiles (box limits), 10th and 90th percentiles (whiskers).