Published February 7, 2023
| Version v1
Dataset
Open
Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome
- 1. Institute of Science and Technology, Am Campus 1, 3400 Klosterneuburg, Austria
- 2. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- 3. Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ, USA; Department of Developmental and Stem Cell Biology, CNRS UMR3738, Institut Pasteur, Paris, France,
- 4. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ, USA; Department of Developmental and Stem Cell Biology, CNRS UMR3738, Institut Pasteur, Paris, France,
Description
This repository contains the trajectory data from "Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome".
Data sets
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:
- data_line0.csv: parS-homie-evePr-PP7, 58 kb
- data_line1.csv: parS-homie-evePr-PP7, 82 kb
- data_line2.csv: parS-homie-evePr-PP7, 88 kb
- data_line3.csv: parS-homie-evePr-PP7, 149 kb
- data_line4.csv: parS-homie-evePr-PP7, 190 kb
- data_line5.csv: parS-homie-evePr-PP7, 595 kb
- data_line6.csv: parS-homie-evePr-PP7, 3.3 Mb
- data_line3_5s.csv: parS-homie-evePr-PP7, 149 kb, 5 second time interval
- data_line0_nohomie.csv: parS-lambda-evePr-PP7, 58 kb
- data_line3_nohomie.csv: parS-lambda-evePr-PP7, 149 kb
Structure of Data
The trajectory data are provided as csv files consisting of 13 columns. The column headers are:
- cell_id: a unique cell index
- time_point: the time frame
- x_blue: x-coordinate of the locus in the blue channel (units in nm)
- y_blue: y-coordinate of the locus in the blue channel (units in nm)
- z_blue: z-coordinate of the locus in the blue channel (units in nm)
- x_green: x-coordinate of the locus in the green channel (units in nm)
- y_green: y-coordinate of the locus in the green channel (units in nm)
- z_green: z-coordinate of the locus in the green channel (units in nm)
- x_Rij: x-component of the aberration corrected 3D distance vector connecting the blue and green loci (units in nm)
- y_Rij: y-component of the aberration corrected 3D distance vector connecting the blue and green loci (units in nm)
- z_Rij: z-component of the aberration corrected 3D distance vector connecting the blue and green loci (units in nm)
- red: intensity in the red channel (a.u.)
- state: inferred state using a 3-state HMM, with entries 0 (O_off), 1 (P_off), 2 (P_on)
Files
data_line0.csv
Files
(10.9 MB)
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