Lagage et al, 2022: Adaptation delay causes a burst of mutations in bacteria responding to oxidative stress
The data are described in the article “Adaptation delay causes a burst of mutations in bacteria responding to oxidative stress." For microfluidics experiments, datasets are separated in folders, each corresponding to one figure or to different panels of a figure of the article (figure and panel...
| Main Authors: | , , |
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| Format: | Dataset |
| Language: | English |
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University of Oxford
2022
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| _version_ | 1797107682342076416 |
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| author | Lagage, V Uphoff, S Chen, V |
| author2 | Uphoff, S |
| author_facet | Uphoff, S Lagage, V Uphoff, S Chen, V |
| author_sort | Lagage, V |
| collection | OXFORD |
| description | The data are described in the article “Adaptation delay causes a burst of mutations in bacteria responding to oxidative stress." For microfluidics experiments, datasets are separated in folders, each corresponding to one figure or to different panels of a figure of the article (figure and panel numbers indicated in each folder name). In each folder are the files of the different repeats performed for the indicated figure/panel. The file names are composed of the name of the strain, and of the frame number corresponding to the start of hydrogen peroxide treatment specific to each experiment. Data are in MATLAB struct array format (.mat) with a separate line for each field of view. Each line is a struct array containing the following fields for each cell in the field of view: cellNo (number of the cell), area (segmented cell area in pixels), Frame No (number of the frame, frame 0 is the first frame of the experiment), MajorAxislength (in pixels), MinorAxislength (in pixels), cenX (centroid X), CenY (centroid Y), mCherryAvg (average mCherry (mKate2) pixel intensity within segmented cell area (a.u.)), mCherrytot (total mCherry (mKate2) pixel intensity, within segmented cell area (a.u.)). YFPAvg (average YFP pixel intensity within segmented cell area (a.u.)), YFPTot (total YFP pixel intensity, within segmented cell area (a.u.)), CFPAvg (average CFP pixel intensity within segmented cell area (a.u.)), CFPTot (total CFP pixel intensity, within segmented cell area (a.u.)), fociNo (number of foci for each frame (1 for frames with a new MutL-mYPet focus, 0 otherwise))), fociIntensity (pixel intensity within foci area (a.u.)), divTimes (frame at which cell division occurs), divDurations (number of frames in between two divisions), CellPhase (fraction of cell cycle at each frame (starting from 0 after division and until 1 just before the next division)), divLeftOver (number of frames left after the last cell division at the end of the experiment). For single-molecule experiments, the folders contain .tracks files labelled with the name of the strain and the time of hydrogen peroxide treatment when needed. We have also included an Excel file named “fractionofboundmoleculesoxyrhalo-pol1halo-dfurpol1halo”, containing the value of the fraction of bound molecules for the relevant strains in untreated and hydrogen peroxide-treated conditions. A MATLAB file named “Matlab figure plotting scripts“ contains the scripts to plot the microfluidics data (generation time, mismatch rate plot, CFP average response curves, survival time distribution, elongation rate, CFP expression rate plots, cell length) and a script to plot diffusion coefficient histograms from the tracks files. For rifampicin assays, the number of colonies counted on LB and LB + rifampicin plates for each repeat are given in an excel file named “rifassaydata-figEV3”. |
| first_indexed | 2024-03-07T07:19:19Z |
| format | Dataset |
| id | oxford-uuid:16808a32-c198-4d70-988c-3b214e287ad8 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T07:19:19Z |
| publishDate | 2022 |
| publisher | University of Oxford |
| record_format | dspace |
| spelling | oxford-uuid:16808a32-c198-4d70-988c-3b214e287ad82022-09-16T18:02:01ZLagage et al, 2022: Adaptation delay causes a burst of mutations in bacteria responding to oxidative stressDatasethttp://purl.org/coar/resource_type/c_ddb1uuid:16808a32-c198-4d70-988c-3b214e287ad8EnglishHyrax DepositUniversity of Oxford2022Lagage, VUphoff, SChen, VUphoff, SChen, VThe data are described in the article “Adaptation delay causes a burst of mutations in bacteria responding to oxidative stress." For microfluidics experiments, datasets are separated in folders, each corresponding to one figure or to different panels of a figure of the article (figure and panel numbers indicated in each folder name). In each folder are the files of the different repeats performed for the indicated figure/panel. The file names are composed of the name of the strain, and of the frame number corresponding to the start of hydrogen peroxide treatment specific to each experiment. Data are in MATLAB struct array format (.mat) with a separate line for each field of view. Each line is a struct array containing the following fields for each cell in the field of view: cellNo (number of the cell), area (segmented cell area in pixels), Frame No (number of the frame, frame 0 is the first frame of the experiment), MajorAxislength (in pixels), MinorAxislength (in pixels), cenX (centroid X), CenY (centroid Y), mCherryAvg (average mCherry (mKate2) pixel intensity within segmented cell area (a.u.)), mCherrytot (total mCherry (mKate2) pixel intensity, within segmented cell area (a.u.)). YFPAvg (average YFP pixel intensity within segmented cell area (a.u.)), YFPTot (total YFP pixel intensity, within segmented cell area (a.u.)), CFPAvg (average CFP pixel intensity within segmented cell area (a.u.)), CFPTot (total CFP pixel intensity, within segmented cell area (a.u.)), fociNo (number of foci for each frame (1 for frames with a new MutL-mYPet focus, 0 otherwise))), fociIntensity (pixel intensity within foci area (a.u.)), divTimes (frame at which cell division occurs), divDurations (number of frames in between two divisions), CellPhase (fraction of cell cycle at each frame (starting from 0 after division and until 1 just before the next division)), divLeftOver (number of frames left after the last cell division at the end of the experiment). For single-molecule experiments, the folders contain .tracks files labelled with the name of the strain and the time of hydrogen peroxide treatment when needed. We have also included an Excel file named “fractionofboundmoleculesoxyrhalo-pol1halo-dfurpol1halo”, containing the value of the fraction of bound molecules for the relevant strains in untreated and hydrogen peroxide-treated conditions. A MATLAB file named “Matlab figure plotting scripts“ contains the scripts to plot the microfluidics data (generation time, mismatch rate plot, CFP average response curves, survival time distribution, elongation rate, CFP expression rate plots, cell length) and a script to plot diffusion coefficient histograms from the tracks files. For rifampicin assays, the number of colonies counted on LB and LB + rifampicin plates for each repeat are given in an excel file named “rifassaydata-figEV3”. |
| spellingShingle | Lagage, V Uphoff, S Chen, V Lagage et al, 2022: Adaptation delay causes a burst of mutations in bacteria responding to oxidative stress |
| title | Lagage et al, 2022: Adaptation delay causes a burst of mutations in bacteria responding to oxidative stress |
| title_full | Lagage et al, 2022: Adaptation delay causes a burst of mutations in bacteria responding to oxidative stress |
| title_fullStr | Lagage et al, 2022: Adaptation delay causes a burst of mutations in bacteria responding to oxidative stress |
| title_full_unstemmed | Lagage et al, 2022: Adaptation delay causes a burst of mutations in bacteria responding to oxidative stress |
| title_short | Lagage et al, 2022: Adaptation delay causes a burst of mutations in bacteria responding to oxidative stress |
| title_sort | lagage et al 2022 adaptation delay causes a burst of mutations in bacteria responding to oxidative stress |
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