Extended Data Fig. 3: Extending the SLICE model parameters to include additional metrics.
From: Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C
a, SLICE can be generalized to account for complex nuclear shapes. As a case study, we considered spheroids (that is, ellipsoids with two equal axes), which we parametrized by the flattening parameter (the relative difference of the radii). b, Relationship between the minimum number of tubes required (m*), genomic resolution and sensitivity. c, m* as a function of XNP and the interaction probability (Pi) given perfect detection efficiency, a genomic distance of 10Mb and h=220 nm, at 30 kb resolution. Dashed black line marks the approximate position of the minimum value of m* across each row. d, Co-segregation frequency of pairs of loci (M2) derived by SLICE as function of the flattening parameter in spheroidal nuclei of constant volume, for different values of interaction frequency (Pi) given slice thickness (h) of 220 nm, resolution of 30 kb, detection efficiency of 1 and genomic distances of 50 Mb. e, Optimal value of XNP and the corresponding value of m* for a range of possible slice thicknesses given Pi =30%, genomic distance of 10Mb and perfect detection. f, Required number of tubes (m*) as a function of XNP and the genomic distance given perfect detection, Pi=50% and h=220 nm, at 30 kb resolution. Dashed black line marks the position of the minimum value of m* across each row.
