Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging

Dataset description

This dataset contains coordinates of the two anchors of a 150 kb simulated loop.

The subfolder 'Free' contains coordinates from a polymer not submitted to loop extrusion (1,000 independent simulations). The subfolder 'Loop' contains loop anchor coordinates in a polymer submitted to loop extrusion (4,000 independent simulations). In simulations with extrusion, the polymer chain was simulated such as it went through 3 different states : i) Open state  (absence of loops) ii) Extruding state where the loop size increases with time (anchor-anchor distance decreases) and iii) Closed state corresponding to a stable loop with the two anchors in contact.

Structure of data

In each .txt file, the first three columns correspond to the XYZ coordinates of the anchor (in µm), the fourth column indicates the state label (0=Open, 1=Extruding, 2=Closed). Each row corresponds to a simulation timepoint (2991 timepoints in polymers submitted to loop extrusion).

The simulation ID is indicated at the end of each .txt file.

The two anchors of the loop are bead #275 and bead #324.