DOI: 10.5281/zenodo.18019781
title: Source data for Kinetic organization of the genome revealed by ultra-resolution, multiscale live imaging

description: # Tracking data 

This repository includes the x,y,z data for pairs of fluorescently labeled DNA in mouse embryonic stem cells, as described in our recent publication:

## Kinetic organization of the genome revealed by ultraresolution multiscale live imaging. Lee, J., Chen, L.-F., Gaudin, S., Gupta, K., Novacic, A., Spakowitz, A. & Boettiger, A. N. Science 389, (2025)  Please note - the previous version of this data contained an error that effected the export of the z-data.  

The data are organized as follows: 

### Region1_XYZT_data.zipRegion 1 contains 11 different label pairs, each imaged with and without depletion of RAD21 (cohesin complex).  In each of the 11 pairs, the second label is at a greater genomic separation from the first.The experiment file name indicates the chemical treatment ("untreated" or "RAD21depleted"), the genomic distance between the probes, and the replicate ID.

### Region1_XYZT_data.zipRegion 2 contains 4 different labels. One pair are 100 kb apart and within the same TAD, the next 100 kb apart yet separated by a TAD border.  The other two pairs contain labels 400 kb apart, one pair within a TAD, the other across the border.The experiment filename indicates datasets from region 2 with the prefix Reg2.  The filename also indicates if the labels cross a TAD border "crossTAD1" or are within the same TAD "crossTAD0", and indicate the genomic separation and treatment status, and replicate number, as for the first set.

### CSV filesWithin each CSV file is a table with the following columnsFrame,X1,Y1,Z1,X2,Y2,Z2,dXY,dXYZ,CellCycleG1,Cell_ID,time

These columns respectively record the frame number, the x,y,z positions of spot 1 and spot 2 in nanometers, the 2D distances between the X,Y coordinates of the two spots, the 3D distance between the 2 spots (analyzed in the paper), the cell cycle state (G1/unreplicated = 1, G2/replicated = 0), the ID number of the cell for that table, and the time (measured in seconds).

### Region1_Any_data.zip  and Region2_Any_data.zipDue to tradeoffs from the fast z-scan both spot pairs are not continuously in the range where the z position can be determined, leading to gaps in the data. While the publication focused on analysis only the subset of time points where a 3D location for each fluorescent spot was obtained, the data where one or both of the spots was localized in 2D or 3D may also be useful. These files are much larger and are available upon request (they are currently not uploading).

The locations of the probes in each experiment are indicated below, and are described in more detail in the manuscript. 

| Experiment | Separation | Label 1 Position | Label 2 Position || exp01 | 5 kb |  chr6:51320704 | chr6:51321893 || exp02 | 5 kb |  chr6:51320704 | chr6:51321893 || exp03 | 20 kb |  chr6:51320704 | chr6:51336653 || exp04 | 20 kb |  chr6:51320704 | chr6:51336653 || exp05 | 55 kb |  chr6:51320704 | chr6:51371176 || exp06 | 55 kb |  chr6:51320704 | chr6:51371176 || exp07 | 70 kb |  chr6:51320704 | chr6:51387332 || exp08 | 70 kb |  chr6:51320704 | chr6:51387332 || exp09 | 134 kb |  chr6:51320704 | chr6:51451617 || exp10 | 134 kb |  chr6:51320704 | chr6:51451617 || exp11 | 260 kb |  chr6:51320704 | chr6:51576421 || exp12 | 260 kb |  chr6:51320704 | chr6:51576421 || exp13 | 407 kb |  chr6:51320704 | chr6:51724680 || exp14 | 407 kb |  chr6:51320704 | chr6:51724680 || exp15 | 799 kb |  chr6:51320704 | chr6:50525643 || exp16 | 799 kb |  chr6:51320704 | chr6:50525643 || exp17 | 2030 kb |  chr6:51320704 | chr6:49294139 || exp18 | 2030 kb |  chr6:51320704 | chr6:49294139 || exp19 | 12795 kb |  chr6:51320704 | chr6:38529185 || exp20 | 12795 kb |  chr6:51320704 | chr6:38529185 || exp21 | 73567 kb |  chr6:51320704 | chr6:124883209 || exp22 | 73567 kb |  chr6:51320704 | chr6:124883209 || exp23 | 95 kb | chr15:11568485    |    chr15:11477063 || exp24 | 95 kb | chr15:11568485    |    chr15:11477063 || exp25 | 108 kb | chr15:11373113    |    chr15:11477063 || exp26 | 108 kb | chr15:11373113    |    chr15:11477063 || exp27 | 409 kb | chr15:11071425    |    chr15:11477063 || exp28 | 409 kb | chr15:11071425    |    chr15:11477063 || exp29 | 407 kb |  chr15:11880005    |    chr15:11477063 || exp30 | 407 kb |  chr15:11880005    |    chr15:11477063 |