Fig. 4: Combining 3DRAM-seq with immunoFACS enables multimodal profiling of the cell-type-specific epigenetic landscape in human cortical organoids. | Nature Cell Biology

Fig. 4: Combining 3DRAM-seq with immunoFACS enables multimodal profiling of the cell-type-specific epigenetic landscape in human cortical organoids.

From: Joint epigenome profiling reveals cell-type-specific gene regulatory programmes in human cortical organoids

Fig. 4

a, Experimental overview of human cortical organoid generation followed by the isolation of RGCs and IPCs by immunoFACS. D, day; EB, embryoid body. b, Representative immunofluorescence image of a neural rosette formed within a cortical organoid at day 45. Scale bar, 10 µm. c, Scatterplot depicting significantly (false discovery rate (FDR) < 0.05) upregulated or downregulated genes in RGC-to-IPC differentiation. Purple, genes upregulated in IPC compared to RGC. Green, genes downregulated in IPC. d, GO term enrichment (biological processes) of differentially regulated genes. Colour and size of circles indicate Benjamini–Hochberg adjusted P value (hypergeometric test) and number of genes, respectively. e,f, CpG methylation (e) and GpC accessibility (f) levels at CTCF-motif-centred GpC peaks for RGCs and IPCs. g, Contact maps (top) and CpG methylation and GpC accessibility levels (bottom) for chromosome 3 (200 kb bins). h, Average contact enrichment, CpG methylation and GpC accessibility levels at TADs for RGCs and IPCs. i, Contact maps, GpC accessibility, DNA methylation and expression levels for RGCs and IPCs at the SOX2 locus. Black dotted circles and boxes in the genomic tracks indicate putative CREs.

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