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

<p><strong>Dataset description</strong></p> <p>This dataset contains coordinates of the two anchors of a 150 kb simulated loop (static imaging) and anchor-anchor distances of a 150 kb loop in simulations where the extruder was allowed to unbind from the polymer (dynamic imaging).</p> <p><strong>Dataset description - Static imaging</strong></p> <p>This dataset contains coordinates of the two anchors of a 150 kb simulated loop.</p> <p>The subfolder &#39;Free&#39; contains coordinates from a polymer not submitted to loop extrusion (1,000 independent simulations). The subfolder &#39;Loop&#39; 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&nbsp; (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.</p> <p>&nbsp;</p> <p><strong>Structure of data - Static imaging</strong></p> <p>In each .txt file, the first three columns correspond to the XYZ coordinates of the anchor (in &micro;m), 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).</p> <p>The simulation ID is indicated at the end of each .txt file.</p> <p>The two anchors of the loop are bead #275 and bead #324.</p> <p>&nbsp;</p> <p><strong>Structure of data - Dynamic imaging</strong></p> <p>Each .txt file contains the anchor-anchor distance (in &micro;m) as function of time for approximately 10,000 independent simulations. Each column is an independent simulation. Each row is a simulation timepoint (0.3 s / simulation unit). The different .txt files correspond to different localization errors, indicated in &micro;m in XY and Z.</p> <p>&#39;list_deb_closed_10000.p&#39; is a dictionary whose keys are the simulation ID (corresponding to the columns of the .txt files), and the values are the frame at which extrusion begins.</p> <p>&#39;list_end_closed_10000.p&#39; is a dictionary whose keys are the simulation ID (corresponding to the columns of the .txt files), and the values are the frame at which extrusion ends.</p>