Extended Data Fig. 3: Comparison of in vitro and in vivo identified LADs.
From: Distinct nuclear compartment-associated genome architecture in the developing mammalian brain
a, Venn diagram showing percent overlap of LAD coverage between brain NPCs and in vitro NPCs (DamID). b, Representative micrographs of DNA-FISH (red) with LaminB ICC (green) in brain NPCs and SVZ-cNSCs for four loci previously annotated as cLADs. Scale bar 2 𝜇m. Multiple images were taken to quantitate sub-nuclear localization of the DNA-FISH loci. c, Quantifications of DNA-FISH for loci shown in b. Percentages indicate loci within 0.5 μm (grey area) from the nuclear lamina. 50-60 nuclei were quantified for each locus. d, LaminB GO-CaRT tracks in brain NPCs, SVZ-cNSCs and in vitro NPCs (DamID) over cLAD DNA-FISH loci (dashed box) shown in b. e, LaminB GO-CaRT tracks of brain NPCs, E13 lung, E13 liver, SVZ-cNSCs and 3T3 MEFs. In vitro NPC and cLAD track (shown on top) are DamID derived6. Dashed box indicates a region where some previously annotated “cLADs” are not observed in tissues in vivo but detected by GO-CaRT in SVZ-NSCs and 3T3 MEFs. f, Venn diagram showing percent overlap of LAD coverage between cLADs and LADs common to brain, lung and liver.
