Figure EV3. Additional information on conditional knockouts.

1. Loop strengths were calculated using the three 60 × 60 kb square regions shown. The average value within the middle box (black) was divided by the average of the combined top‐left and bottom‐right (green) boxes. The resulting number was subtracted by 1 to indicate the fractional increase in loop strength above the background.
2. Immunofluorescence staining of Scc1 in in situ fixed Scc1 ^fl (n = 11) and Scc1 ^∆ zygotes (n = 12, from one experiment using two females of each genotype). DNA in magenta; Scc1 in gray/green. Images were adjusted in brightness/contrast in the individual channels using ImageJ. Scale bars: 10 μm. Left: single z‐slice of zygotes. Right: single z‐slice of the maximum cross‐sectional area of maternal and paternal nuclei. Cropped area is indicated.
3. Loops, TADs, and compartment saddle plots for the Scc1 ^fl, Wapl ^fl, Scc1 ^∆, and WaplΔ conditions are shown separately for the maternal and paternal data. The average strength of each feature is indicated in each panel. Data shown are based on n(Wapl ^fl, maternal) = 7, n(Wapl ^fl, paternal) = 6, n(WaplΔ, maternal) = 8, n(WaplΔ, paternal) = 7, n(Scc1 ^fl, maternal) = 13, n(Scc1 ^fl, paternal) = 17, n(Scc1 ^∆) = 28, and n(Scc1 ^∆) = 17 nuclei, from at least two independent experiments using two to three females per genotype each.
4. Insulation scores calculated with a sliding diamond of size 40 kb, with the “zero” position denoting a domain boundary identified previously in CH12‐LX cells (Rao et al, 2014). Distances are reported in base pairs from a domain boundary. The average over all domain boundaries is reported; error bars are the standard error on the mean insulation score.

Source data are available online for this figure.