Extended Data Figure 4: Deletion of Nipbl in this study leads to more robust disappearance of TADs and associated peaks than in previous publications. | Nature

Extended Data Figure 4: Deletion of Nipbl in this study leads to more robust disappearance of TADs and associated peaks than in previous publications.

From: Two independent modes of chromatin organization revealed by cohesin removal

Extended Data Figure 4

a, Genetic deletion of Nipbl in hepatocytes (this study). b, Deletion of Rad21 in thymocytes20. c, Proteolytic cleavage of RAD21 in HEK293T cells19. d, e, Deletion of Rad21 in NSCs and astrocytes (ASTs)21. For each data set: top, average Hi-C map around 102 peaks with size range 500–600 kb12 in wild-type and ΔNipbl contact maps; middle, average Hi-C map of TADs called in each data set; bottom, relative contact probability between pairs of peak loci versus genomic distance, compared to randomly selected pairs of loci. The thick line shows the median contact probability; the shading shows the envelope between the 25th and 75th percentiles of contact probability at each genomic separation. Note substantial change in the contact probability at peaks (red line) upon Nipbl depletion (a) and little change in other studies (be). All studies used comparable Hi-C sequencing depth (Supplementary Table 3).

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