Extended Data Figure 10. Design and validation of FISH probes for quantification of compartments.

a, FISH probe design for quantifying compartment segregation; left: exact locations of designed probes, right: probe locations are shown superimposed on the Hi-C data (200 kb resolution) from F123 ES cells³⁰ b, probe locations shown relative to the profile of compartment strength (200 kb resolution) as measured by the first eigenvector of the Hi-C map’s eigenvector decomposition. c–d, top: nearest neighbour FISH distances - the same as curves in Figure 4d, but shown for (c) ES cells (n(replicate1)=87, n(replicate2)=78) and (d) maternal (n=33) and paternal (n=37) zygotic nuclei; bottom: z-scores showing the number of standard deviations from the expected minimum distance distribution of the control data; the control distribution was obtained from randomly reshuffling probe colours as described in the methods.