A master regulator orchestrates bacterial stress response genes in space and time

This material relates to the article ‘A master regulator orchestrates bacterial stress response genes in space and time’' 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 detailed in Choudhary et al. Cell Rep. 2023 (doi: 10.1016/j.celrep.2023.112168) and Choudhary et al. Curr. Bio. 2023 (doi: 10.1016/j.cub.2023.11.002). This folder contains:
(A) Experiment_List: Excel file listing the experiments, including Experiment_ID (enumaerated 1 to 80), Promoter analysed, strain (WT: wild type, or Katg-), H2O2 concentration, Treatment type (step or gradual), treatment time, Start_ROI (Positions greater than this are analysed), and Stop_ROI (Positions smaller than this are analysed).
(B) The output files obtained from BACMMAN for all experiments described 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 E1 to E80, corresponding to the experiments listed in Excel file (A) .
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.
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 or GFP fluorescence inside the segmented cell masks. 3 relates to measurements of YFP fluorescence inside the segmented cell masks (For dual reporter strains). The folder also contains the BACMMAN config file used for each experiment.