Phenotypic heterogeneity in the bacterial oxidative stress response is driven by cell-cell interactions
This material relates to the article 'Phenotypic heterogeneity in the bacterial oxidative stress response is driven by cell-cell interactions' by Choudhary et al. The quantitative microscopy data collected from the microfluidics imaging experiments were processed using BACMMAN software (Ol...
| Main Authors: | , , , |
|---|---|
| Format: | Dataset |
| Language: | English |
| Published: |
University of Oxford
2023
|
| _version_ | 1826309304072798208 |
|---|---|
| author | Choudhary, D Uphoff, S Foster, K Lagage, V |
| author2 | Choudhary, D |
| author_facet | Choudhary, D Choudhary, D Uphoff, S Foster, K Lagage, V |
| author_sort | Choudhary, D |
| collection | OXFORD |
| description | This material relates to the article 'Phenotypic heterogeneity in the bacterial oxidative stress response is driven by cell-cell interactions' by Choudhary et al. The quantitative microscopy data collected from the microfluidics imaging experiments were processed using BACMMAN software (Ollion et al. Nat Protoc. 2019, 3144-3161. doi: 10.1038/s41596-019-0216-9.) and then processed using custom Python code. This folder contains:
(A) The output files obtained from BACMMAN for all experiments described in the article by Choudhary et al.
(B) Python codes that were used to generate the data plots in the article by Choudhary et al .
Details of the data collection and analysis procedures can be found in the accompanying article.The folders are named as 'Concentration of H2O2 used'_'Promoter'_'Any changes to default experiment protocol'.
Default experiment protocol refers to wild-type E. coli bacteria growing in 1.2 um trenches that were fully loaded and provided with a step treatment of H2O2 and imaged with a time-lag between frames of 3 minutes.
These folders are :
(1)100uM_Pahpc_default
(2)100uM_PgrxA_1p4
(3)100uM_PgrxA_1p4,lowload
(4)100uM_PgrxA_45secResolution
(5)100uM_PgrxA_default
(6)100uM_PgrxA_DoxyRandWTmix
(7)100uM_PgrxA_InactiveWTmix
(8)100uM_PgrxA_Lowloading
(9)100um_PgrxA_oxyRMutant
(10)100uM_PgrxA_Pulses
(11)100uM_Pkatg_default
(12)500uM_PgrxA_grad
(13)500uM_PgrxA_PIStain
(14)500uM_PgrxA_step
Each of the folders contains subfolders pertaining to different experiments performed in the given conditions. Each subfolder contains BACMMAN output files named as 'SubFolderName'_'0 or 1 or 2 or 3'. Here, 0 relates to measurements of growth channels tracked over time to correct for any drifts while imaging. 1 relates to measurements of the cell mask from the mKate2 cell segmentation marker signal. 2 relates to measurements of CFP fluorescence inside the segmented cell masks. 3 relates to MutL-mYPet foci detection in the segmented cell masks. The folder also contains the BACMMAN config file used for each experiment.
The other folders:
(15) ExperimentsForCalibration: contains the BACMMAN output files of the experiments that were used for calibration experiments performed at different H2O2 concentrations.
(16) ExperimentsForMachineLearningAnalysis: contains BACMMAN output files of experiments for Machine Learning Analysis.
(17) Experiment_details.CSV contains details of each experiment, such as the time of H2O2 treatment and the ROIs used in analysis (annotated as ‘Position’ in the data files).
(18) Figures_codes : contains Python codes for generating the figures in accompanying article.
The subheading in each code file correspond to different panels within the same figures.
|
| first_indexed | 2024-03-07T07:32:12Z |
| format | Dataset |
| id | oxford-uuid:9ec1b346-eadb-4feb-89f8-236837d151f8 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T07:32:12Z |
| publishDate | 2023 |
| publisher | University of Oxford |
| record_format | dspace |
| spelling | oxford-uuid:9ec1b346-eadb-4feb-89f8-236837d151f82023-02-02T14:08:00ZPhenotypic heterogeneity in the bacterial oxidative stress response is driven by cell-cell interactionsDatasethttp://purl.org/coar/resource_type/c_ddb1uuid:9ec1b346-eadb-4feb-89f8-236837d151f8EnglishHyrax DepositUniversity of Oxford2023Choudhary, DUphoff, SFoster, KLagage, VChoudhary, DChoudhary, DUphoff, SFoster, KThis material relates to the article 'Phenotypic heterogeneity in the bacterial oxidative stress response is driven by cell-cell interactions' by Choudhary et al. The quantitative microscopy data collected from the microfluidics imaging experiments were processed using BACMMAN software (Ollion et al. Nat Protoc. 2019, 3144-3161. doi: 10.1038/s41596-019-0216-9.) and then processed using custom Python code. This folder contains: (A) The output files obtained from BACMMAN for all experiments described in the article by Choudhary et al. (B) Python codes that were used to generate the data plots in the article by Choudhary et al . Details of the data collection and analysis procedures can be found in the accompanying article.The folders are named as 'Concentration of H2O2 used'_'Promoter'_'Any changes to default experiment protocol'. Default experiment protocol refers to wild-type E. coli bacteria growing in 1.2 um trenches that were fully loaded and provided with a step treatment of H2O2 and imaged with a time-lag between frames of 3 minutes. These folders are : (1)100uM_Pahpc_default (2)100uM_PgrxA_1p4 (3)100uM_PgrxA_1p4,lowload (4)100uM_PgrxA_45secResolution (5)100uM_PgrxA_default (6)100uM_PgrxA_DoxyRandWTmix (7)100uM_PgrxA_InactiveWTmix (8)100uM_PgrxA_Lowloading (9)100um_PgrxA_oxyRMutant (10)100uM_PgrxA_Pulses (11)100uM_Pkatg_default (12)500uM_PgrxA_grad (13)500uM_PgrxA_PIStain (14)500uM_PgrxA_step Each of the folders contains subfolders pertaining to different experiments performed in the given conditions. Each subfolder contains BACMMAN output files named as 'SubFolderName'_'0 or 1 or 2 or 3'. Here, 0 relates to measurements of growth channels tracked over time to correct for any drifts while imaging. 1 relates to measurements of the cell mask from the mKate2 cell segmentation marker signal. 2 relates to measurements of CFP fluorescence inside the segmented cell masks. 3 relates to MutL-mYPet foci detection in the segmented cell masks. The folder also contains the BACMMAN config file used for each experiment. The other folders: (15) ExperimentsForCalibration: contains the BACMMAN output files of the experiments that were used for calibration experiments performed at different H2O2 concentrations. (16) ExperimentsForMachineLearningAnalysis: contains BACMMAN output files of experiments for Machine Learning Analysis. (17) Experiment_details.CSV contains details of each experiment, such as the time of H2O2 treatment and the ROIs used in analysis (annotated as ‘Position’ in the data files). (18) Figures_codes : contains Python codes for generating the figures in accompanying article. The subheading in each code file correspond to different panels within the same figures. |
| spellingShingle | Choudhary, D Uphoff, S Foster, K Lagage, V Phenotypic heterogeneity in the bacterial oxidative stress response is driven by cell-cell interactions |
| title | Phenotypic heterogeneity in the bacterial oxidative stress response is driven by cell-cell interactions |
| title_full | Phenotypic heterogeneity in the bacterial oxidative stress response is driven by cell-cell interactions |
| title_fullStr | Phenotypic heterogeneity in the bacterial oxidative stress response is driven by cell-cell interactions |
| title_full_unstemmed | Phenotypic heterogeneity in the bacterial oxidative stress response is driven by cell-cell interactions |
| title_short | Phenotypic heterogeneity in the bacterial oxidative stress response is driven by cell-cell interactions |
| title_sort | phenotypic heterogeneity in the bacterial oxidative stress response is driven by cell cell interactions |
| work_keys_str_mv | AT choudharyd phenotypicheterogeneityinthebacterialoxidativestressresponseisdrivenbycellcellinteractions AT uphoffs phenotypicheterogeneityinthebacterialoxidativestressresponseisdrivenbycellcellinteractions AT fosterk phenotypicheterogeneityinthebacterialoxidativestressresponseisdrivenbycellcellinteractions AT lagagev phenotypicheterogeneityinthebacterialoxidativestressresponseisdrivenbycellcellinteractions |