Dataset for "Suppression of bacterial cell death underlies the antagonistic interaction between ciprofloxacin and tetracycline in Escherichia coli"

This dataset contains the fluorescence microscopy image data underlying the study "Suppression of bacterial cell death underlies the antagonistic interaction between ciprofloxacin and tetracycline in Escherichia coli" published as a preprint in BioRxiv (https://doi.org/10.1101/2024.04.18.590101).

The images were captured using Escherichia coli cells trapped in a mother machine microfluidic device (methods also described here https://doi.org/10.15252/msb.202110441).
The aim of these experiments was to evaluate the single-cell physiological response of E coli to exposure to ciprofloxacin (CIP) and tetracycline (TET) combinations using different growth media.

The data is divided into "Compiled_output_data" and the specific "Figure" folders (Figure-1, Figure-2, Figure-3), which contains the image files and data outputs for each experiment separately.

#Compiled_output_data":
Contains the compiled output data from the fluorescence microscopy experiments as described above in both CSV and pickle format. This folder contais a specific README file (README-compiled) with instructions on how to open the compiled data file using the pickle function in Python.

# Figure-1.zip, Figure-2.zip, Figure-3.zip:
Within each main figure data folder, we separated the datasets into two subfolders: "Fluorescence_microscopy_images" and "BACMMAN_outputs". Within each of these folders the data is then divided and named according to the specific figure panels where they first appear and the treatment used (e.g., "1BFI-Glu-aa-control").
Different replicates are shown in the next directory level as for example: "Gluaa-control-1" and "Gluaa-control-2".

-"Fluorescence_microscopy_images": contains the raw image data (TIFF format);
- "BACMMAN_outputs" contains: "Output" folder which has segmented and pre-processed image files from BACMMAN (TIFF and .db formats), the configuration files used in BACMMAN to perform the segmentation and the measurements (files named with suffix "BACMMAN_config"; JSON format), and the data output files containing the quantification results obtained from the images for mKate2 (detected using mCherry filter) and GFP channels [gene expression reporters for SOS expression PsulA-mGFP) and constitutive expression (Ptet01-mKate2)]. The files are named with the suffix "Output_data-GFP" and "Output_data-mKate2"; CSV format).

The same source data that was used in Figs.1-2-3 were also used to produce other analysis, and therefore are related to several other figures in the manuscript. Below we provide the relationship between the source data and publication figures:

Figure-1/1BFI-Glu-aa-control: Fig 1 B,F,I; Fig 2 C; Fig 3 C,D; Fig 4 A; Fig 5 G,H; Fig S4 C; Table S1
Figure-1/1CGJ-Glu-aa-TET: Fig 1 C,G,J; Fig 2 C; Fig 3 C,D; Fig 4 A; Fig 5 G,H; Fig S4 C; Table S1
Figure-1/1DEK-Glu-aa-CIP: Fig 1 D,E,H,K; Fig 2 C; Fig 3 C,D; Fig 4 A,D,G,J; Fig 5 C,F,G,H,I; Fig S4 C; Fig S5 A-F; Fig S9 A; Fig S10 A; Table S1
Figure-2/2ABC-Glu-aa-CIP-TET: Fig 2 A,B,C; Fig 3 C,D; Fig 4 A; Fig 5 C,F,G,H,I; Fig S4 C; Fig S5 G-L; Fig S8 D,G; Fig S9 D; Fig S10 D; Table S1
Figure-3/3BD-Glu-control: Fig 3 B,D; Fig 4 B; Fig 5 G,H; Fig S2 A,E,I; Fig S4 B; Table S1
Figure-3/3BD-Glu-TET: Fig 3 B,D; Fig 4 B; Fig 5 G,H; Fig S2 B,F,I; Fig S4 B; Table S1
Figure-3/3BD-Glu-CIP: Fig 3 B,D; Fig 4 B,E,H,K; Fig 5 B,E,G,H,I; Fig S2 C,G,I; Fig S4 B; Fig S6 A-F; Fig S9 B; Fig S10 B; Table S1
Figure-3/3BD-Glu-CIP-TET: Fig 3 B,D; Fig 4 B; Fig 5 B,E,G,H,I; Fig S2 D,H,I; Fig S4 B; Fig S6 G-L; Fig S8 E,H; Fig S9 E; Fig S10 E; Table S1
Figure-3/3AD-Gly-control: Fig 3 A,D; Fig 4 C; Fig 5 G,H; Fig S3 A,E,I; Fig S4 A; Table S1
Figure-3/3AD-Gly-TET: Fig 3 A,D; Fig 4 C; Fig 5 G,H; Fig S3 B,F,I; Fig S4 A; Table S1
Figure-3/3AD-Gly-CIP: Fig 3 A,D; Fig 4 C,F,I,L; Fig 5 A,D,G,H,I; Fig S3 C,G,I; Fig S4 A; Fig S7 A-F; Fig S9 C; Fig S10 C; Table S1
Figure-3/3AD-Gly-CIP-TET: Fig 3 A,D; Fig 4 C; Fig 5 A,D,G,H,I; Fig S3 D,H,I; Fig S4 A; Fig S7 G-L; Fig S8 F,I; Fig S9 F; Fig S10 F; Table S1

Please refer to the README.txt file for further dataset description and a directory tree.

James Broughton, Meriem El Karoui, Achille Fraisse & Livia Scorza (2024). Dataset for "Suppression of bacterial cell death underlies the antagonistic interaction between ciprofloxacin and tetracycline in Escherichia coli". BioStudies, S-BIAD1260. Retrieved from https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1260