Extended Data Fig. 4: 3DRAM-seq in purified neural progenitors from human cortical organoids.
(A) Gating strategy for the immunoFACS of RGC and IPC from cortical organoids. From left to right: Singlets in G0/G1 based on their DNA content (DAPI) were selected first, followed by separation of nuclei positive for SOX2 or EOMES. SOX2 positive cells were further subdivided based on PAX6. Number represent mean ± SD from the parental singlet population. (B) Bar plot depicting measured methylation levels of lambda (only GpC methylated) and fully methylated puc19 DNA spike-in controls. Black dots: mean of individual biological replicates (n = 2 for each condition); Numbers: mean methylation levels. (C) DNA methylation coverage (100 bp bins) for RGC and IPC. Black dot and whiskers indicate mean ± SD (n = 2). (D-G) Pairwise correlation matrixes displaying correlation coefficient and/or scatterplot for gene expression (D; Spearman’s), DNA methylation (E; Pearson, 10 kb bins), GpC accessibility (F; Pearson, 10 kb bins) and 3D genome (G; stratum adjusted correlation coefficient, 10 kb bins). (H-I) CpG methylation (H) and GpC accessibility (I) levels at motif centered CTCF ChIP-seq peaks derived from the whole human cortex. (J) Contact probability in logarithmic bins for RGC and IPC. Lines: mean values from different methods; semi-transparent ribbons: SEM. (K) Boxplots displaying quantification of intraTAD and interTAD contact enrichment in RGC and IPC (n = 2939 TADs). Statistical significance is calculated using a two-sided paired t-test. Boxplots display median (line), 25th or 75th percentiles (box) as well as 10th or 90th percentiles (whisker). (L) Average contact strength between intraTAD pairs of GpC peaks containing convergent orientated CTCF motifs. Source numerical data are available in source data.
