Fig. 4: Individual validations of top hits.
From: Perturb-tracing enables high-content screening of multi-scale 3D genome regulators
a, Western blot of siCtrl-treated and siCHD7-treated A549-Cas9 nuclear extracts. The experiment was repeated five times with similar results. b, A–B compartment profile of chr22 in siCtrl cells. c, A–B compartment profile of chr22 in siCHD7 cells. d, Polarization indices of chr22 A–B compartments of siCtrl (white) and siCHD7 (orange). Shadowed boxes show the polarization indices from randomized controls, where the compartment identities of TADs are scrambled. e, Compartmental contact frequencies of siCtrl and siCHD7 (shadowed) among A compartment regions (red), between A and B compartment regions (purple) and among B compartment regions (blue). f, log2fc of inter-TAD distance of siCHD7 compared to siCtrl. g, Overall inter-TAD distance of siCtrl and siCHD7. h, Radii of gyration of siCtrl and siCHD7. i, log2fc of short-range and long-range inter-TAD distances between siCHD7 and siCtrl. j, Relative blot intensities of PCBP1 and ZNF114 western blot bands (normalized by loading control actin B bands). Data are presented as mean values ± s.d. Statistics are derived from three biological replicates. k, log2fc of inter-TAD distance of sgPCBP1 compared to sgCtrl. l, Overall inter-TAD distance of sgCtrl and sgPCBP1. m, Compartmental contact frequencies of sgCtrl and sgPCBP1 (shadowed) among A compartment regions (red), between A and B compartment regions (purple) and among B compartment regions (blue). n, log2fc of inter-TAD distance of sgZNF114 compared to sgCtrl. o, Overall inter-TAD distance of sgCtrl and sgZNF114. P values in d, e, h and m were calculated by two-sided Wilcoxon rank-sum test. P values in g, i, l and o were calculated by two-sided Wilcoxon signed-rank test. P value in j was calculated by a two-sided, two-sample t-test. The boxes cover the 25th to 75th percentiles, the whiskers cover the 10th to 90th percentiles, and the lines in the middle of the boxes represent the median values. Number of traces analyzed: 3,181 (siCtrl) and 3,545 (siCHD7) for d and h; 3,558 (siCtrl) and 4,134 (siCHD7) for e–g and i; 4,627 (sgCtrl) and 3,543 (sgPCBP1) for k–m; 4,602 (sgCtrl) and 3,954 (sgZNF114) for n and o. a.u., arbitrary units.
