Extended Data Fig. 7: Analysis of time course replicate 3.
From: A chromosome folding intermediate at the condensin-to-cohesin transition during telophase
a, Aggregated Hi-C data binned at 20 kb resolution at chromatin loops at different time points. Top row: Experimental Hi-C data. Middle row: Simulated Hi-C data. Bottom row: The difference between experimental and simulated Hi-C data. Loops are more prominent in experimental Hi-C data than in the simulated data between 3.25 and 4 hours. This analysis included loops larger than 200 kb to avoid the strong signal at the diagonal of the interaction matrix. Simulations were performed with experimental data from this time course (mixing Hi-C data for t = 0 and t = 6 hours). b, Aggregate Hi-C data binned at 40 kb resolution at TAD boundaries for different time points. Top row: Experimental Hi-C data. Middle row: Simulated Hi-C data. Bottom row: The difference between experimental and simulated Hi-C data. Insulation strength is stronger in experimental Hi-C data than in simulated Hi-C data at t = 3.25 and t = 4 hours. c, Saddle plots of Hi-C data binned at 200 kb resolution for different time points. Top row: Experimental Hi-C data. Middle row: Simulated Hi-C data. Bottom row: The difference between experimental and simulated Hi-C data. Compartmentalization is weaker in experimental Hi-C than in simulated Hi-C data as illustrated by the fact that A-B interactions are less depleted in the experimental data (upper right and lower left corner of saddle plots). d, Derivative from P(s) plots. Black lines represent the derivative of P(s) for experimental Hi-C data and the dashed green lines represent the derivative of P(s) for the simulated Hi-C datasets for corresponding time points. Three independent experiments were performed with similar results.
