Extended Data Fig. 9: Gene expression and chromatin features of SPADs, inter-LAD, nonSPADs and LADs in human cortex.
From: Distinct nuclear compartment-associated genome architecture in the developing mammalian brain
a, Genome-wide scatter plot showing Pearson correlation between SON GO-CaRT in HEK293T cells and SON TSA-seq in K562 cells4. b, Circos plot showing SON GO-CaRT (green) and LaminB GO-CaRT profiles (blue) across the human chromosomes (1-22) in GW20 cortex. SPADs and LADs are shown by green and blue horizontal bars, respectively. c, Box plot depicting average gene expression in LADs (blue, n = 3105), non-speckle inter-LADs (grey, n = 9452) and SPADs (green, n = 8272) as determined by RNA-seq in GW20 human cortex, n = number of genes. P = Wilcoxon rank sum test, two-sided non-adjusted. Boxes show the range from lower (25th percentile) to upper quartiles (75th percentile), with the median line (50th percentile); whiskers extend 1.5 times the inter-quartile range from bounds of box. d, Average enrichment of various chromatin marks48 in LADs (blue), non-speckle inter-LADs (grey) and SPADs (green) in GW20 cortex. Mean enrichment of chromatin marks over each region scaled to the relative size of each region, which is depicted by the black horizontal. Traces in the 25 Kb flanking proximal and distal regions are unscaled.
