Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome

<p>This repository contains the trajectory data from &quot;Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome&quot;.</p> <p><strong>Data sets</strong></p> <p>We provide data sets for the following constructs and imaging conditions, where we give the name of the construct and the MS2-parS genomic separation in kb:</p> <ul> <li>data_line0.csv: parS-homie-evePr-PP7, 58 kb</li> <li>data_line1.csv: parS-homie-evePr-PP7, 82 kb</li> <li>data_line2.csv: parS-homie-evePr-PP7, 88 kb</li> <li>data_line3.csv: parS-homie-evePr-PP7, 149 kb</li> <li>data_line4.csv: parS-homie-evePr-PP7, 190 kb</li> <li>data_line5.csv: parS-homie-evePr-PP7, 595 kb</li> <li>data_line6.csv: parS-homie-evePr-PP7, 3.3 Mb</li> <li>data_line3_5s.csv: parS-homie-evePr-PP7, 149 kb, 5 second time interval</li> <li>data_line0_nohomie.csv: parS-lambda-evePr-PP7, 58 kb</li> <li>data_line3_nohomie.csv: parS-lambda-evePr-PP7, 149 kb</li> </ul> <p><strong>Structure of Data</strong></p> <p>The trajectory data are provided as csv files consisting of 13 columns. The column headers are:</p> <ul> <li>cell_id: a unique cell index</li> <li>time_point: the time frame</li> <li>x_blue: x-coordinate of the locus in the blue channel (units in nm)</li> <li>y_blue: y-coordinate of the locus in the blue channel (units in nm)</li> <li>z_blue: z-coordinate of the locus in the blue channel (units in nm)</li> <li>x_green: x-coordinate of the locus in the green channel (units in nm)&nbsp;&nbsp;</li> <li>y_green: y-coordinate of the locus in the green channel (units in nm)</li> <li>z_green: z-coordinate of the locus in the green channel (units in nm)&nbsp;&nbsp;</li> <li>x_Rij: x-component of the aberration corrected 3D distance vector connecting the blue and green loci (units in nm)</li> <li>y_Rij: y-component of the aberration corrected 3D distance vector connecting the blue and green loci (units in nm)</li> <li>z_Rij: z-component of the aberration corrected 3D distance vector connecting the blue and green loci (units in nm)</li> <li>red: intensity in the red channel (a.u.)</li> <li>state: inferred state using a 3-state HMM, with entries 0 (O_off), 1 (P_off), 2 (P_on)</li> </ul>