Supplementary Figure 7: 5C heatmaps and boxplots of the engineered de novo loop after 24 h of blue light illumination in independent experiments.

(a-e) Zoomed-in 5C heatmaps represent engineered de novo loop between the targeted Zfp462 promoter (chr4:54,911,136–54,983,136; vertical) and pluripotency-specific Klf4 SE (chr4:55,451,136–55,523,136; horizontal) regions in LADL-engineered mouse ES cells after 24 h of (a, c-e) 5 mW/cm² or (b) 1.5 mW/cm² intensity blue light illumination, or in dark, from independent replicate experiments. (a-e) The loop is represented in relative interaction frequencies (top rows) and distance-corrected interaction scores (bottom rows). (a, c-d) Empty target controls (Anchor + Bridge) in dark are included in replicate 1, replicates 3–4. (b) Empty anchor control (Bridge + Target) in replicate 2 and (c) one-sided guide control (Anchor + Bridge + Zfp462 promoter only Target) in replicate 3 were exposed to the blue light for 24 h, or were in dark. See Supplementary Figure 1 for details of the plasmid combinations used. (f) Boxplots of relative interaction frequencies in the de novo engineered loop pixels (green box in a-e) from each independent experiment, respectively. Boxplots: central tendency = median, box minima = 25th percentile, box maxima = 75th percentile, notches = 95% confidence interval, whiskers = 1.5x interquartile range.