DOI: 10.5281/zenodo.11401114
title: Data with paper "Size Laws and Division Ring Dynamics in Filamentous Escherichia coli cells"

description: See also the other Zenodo record: https://zenodo.org/records/11401470

 

Data files related to manuscript:

Wehrens M, Ershov D, Rozendaal R, Walker N, Schultz D, Kishony R, Levin PA, Tans SJ (2018). “Size Laws and Division Ring Dynamics in Filamentous Escherichia coli cells”. Current Biology.

https://doi.org/10.1016/j.cub.2018.02.006

 

Currently, single cell experimental time trace data for figures 1, 2 and 4 is added. Additional data will follow.

 

Scripts are available at:

https://github.com/TansLab/Tans_filamentation

 

And you will also need the additional scripts from the repositories:

https://github.com/TansLab/Common_libraries

https://github.com/TansLab/Tans_Schnitzcells

 

Script that generates figures:

https://github.com/TansLab/Tans_filamentation/blob/master/ershovwehrensallfigures.m

 

And more specifically, data is loaded, (partially analyzed,) and plotted here:

https://github.com/TansLab/Tans_filamentation/blob/master/script20160429_filamentRecoveryDivisionRatioss.m

 

Description of the .mat files

 

These .mat files contain the lineage information, which were used to generate figures 1 and 2.

 

Each row corresponds to a cell from birth to division.

 

Most important fields are:

P is its parent cell (number referring to the row of the table).

E is the daughter cell after this cell divides

D is the other daughter cell after this cell divides

frame_nrs is in which frame this cell lived

areapx is its area in pixels

 

Different methods were used to determine the bacterias length. For the tetracycline experiments, often the field “length_fitNew” was used, which is a higher order polynomial fitted through the bacterium. For the other stress conditions, mostly the field “length_skeleton” was used, which is the length of the skeleton of the bacteria, extrapolated until it reaches the bacterial edge (this was done because in those experiments, these bacteria often had weird shapes that couldn’t be fitted by polynomials).

 

The growth rate of the bacteria is determined by fitting an exponential curve through length information of multiple frames. Given the fluctuation of growth rates, sometimes bacteria grow relatively slow over a certain amount of frames, or relatively fast. Therefor, sometimes the fit is done using more or less frames. The growth rate information can be found in e.g. the parameters 'muP15_fitNew_all','muP9_skeleton_all','muP5_skeleton_all', where mu refers to growth rate, PX indicates X frames around the frame of interest were used for the fit, and fitNew_all or skeleton_all refers respectively to which length parameter was used for the fit.

 

Note that birth sizes and interdivision times, as wel as added length, can be calculated from the above parameters using the data structure. (See also applicable scripts.)

 

The data also contains more fields with information about length and size, and also fields for fluorescence data. The latter is not really applicable here. 

 

See also the methods section of the paper for more information.

 

INFORMATION ABOUT THE DATA

 

Files for the SulA condition:






Data file



Switch time from stress to stress-free condition (min)





\2016-04-08_FilaRecovery_sulA_recovery_200uM_IPTG\pos1crop\data\pos1crop-Schnitz.mat



0





\2016-04-08_FilaRecovery_sulA_recovery_200uM_IPTG\pos2crop\data\pos2crop-Schnitz.mat



0





\2016-04-08_FilaRecovery_sulA_recovery_200uM_IPTG\pos3crop\data\pos3crop-Schnitz.mat



0





\2016-04-08_FilaRecovery_sulA_recovery_200uM_IPTG\pos4crop\data\pos4crop-Schnitz.mat



0





\2016-04-08_FilaRecovery_sulA_recovery_200uM_IPTG\pos7crop\data\pos7crop-Schnitz.mat



0





If switch time is zero, recording started at the switch time.

 

For the temperature condition






Data file



Switch time from stress to stress-free condition (min)





2016-03-23_FilaRecovery_asc777_42C\pos4crop\data\pos4crop-Schnitz.mat



450





2016-04-07_FilaRecovery_asc777\pos2crop\data\pos2crop-Schnitz.mat



329





 

Delta min tetracycline condition






Data file



Switch time from stress to stress-free condition (min)





2017-09-22_FilaRecovery_asc1035_DeltaMinCDE\pos1cropb\data\pos1cropb-Schnitz.mat



5





2017-09-22_FilaRecovery_asc1035_DeltaMinCDE\pos2cropa\data\pos2cropa-Schnitz.mat



5





2017-09-22_FilaRecovery_asc1035_DeltaMinCDE\pos2cropb\data\pos2cropb-Schnitz.mat



5





2017-09-22_FilaRecovery_asc1035_DeltaMinCDE\pos2cropc\data\pos2cropc-Schnitz.mat



5





2017-09-22_FilaRecovery_asc1035_DeltaMinCDE\pos3cropa\data\pos3cropa-Schnitz.mat



5





 

Tetracycline data

Only data sets 1 to 5 where used here

   






Data file



Switch time from stress to stress-free condition (min)





F schijf AmolfBackup_3april2014\USE_DIV\1uM_pos3_long.mat



890.9800 





F schijf AmolfBackup_3april2014\USE_DIV\1uM_pos4.mat



404.7500        





F schijf AmolfBackup_3april2014\USE_DIV\1uM_pos4_long.mat



0 





F schijf AmolfBackup_3april2014\USE_DIV\1uM_pos5.mat



529.7600 





F schijf AmolfBackup_3april2014\USE_DIV\1uM_pos5_long.mat



0





F schijf AmolfBackup_3april2014\USE_DIV\2uM_pos2.mat



NA





F schijf AmolfBackup_3april2014\USE_DIV\2uM_pos4.mat



NA





F schijf AmolfBackup_3april2014\USE_DIV\2uM_pos6.mat



NA





F schijf AmolfBackup_3april2014\USE_DIV\10uM_pos1.mat



NA





F schijf AmolfBackup_3april2014\USE_DIV\10uM_pos3.mat



NA





F schijf AmolfBackup_3april2014\USE_DIV\10uM_pos6_long.mat



NA





 

Tetracycline data 2 (redundant with above)

 






Data file



Switch time from stress to stress-free condition (min)





2013-12-09\pos3crop\data\pos3crop-Schnitz.mat



890.9800 





2013-09-24\pos4crop\data\pos4crop-Schnitz.mat



404.7500        





2013-12-16\pos4crop\data\pos4crop-Schnitz.mat



0 





2013-09-24\pos5crop\data\pos5crop-Schnitz.mat



529.7600 





2013-12-16\pos5crop\data\pos5crop-Schnitz.mat



0