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

This dataset contains growth data of E. coli cells measured by optical density at a wavelenght of 600 nm (OD600) to determine the conditions where the combination of ciprofloxacin (CIP) and tetracycline (TET) is antagonistic (or suppressive), using a medium that supports fast growth (M9 based medium supplemented with glucose and amino acid). Two types of assays were performed: a checkerboard assay with a 2-dimension gradient of antibiotic concentrations shown in "Fig-S1AB-Growth_rates-Checkerboard_assay.zip", and bulk growth rates assay shown in "Fig-S1C-Bulk_doubling_rates-Bioreactor.zip". These experiments are presented in the supplementary figures of the following manuscript published as preprint in bioRxiv: https://doi.org/10.1101/2024.04.18.590101. Fig-S1AB-Growth_rates-Checkerboard_assay.zip: - growth-OD600-Blank_correct.xlsx: contains the blank corrected (subtracted by initial OD of sterile medium) OD600 data for each well measured in the checkerboard assay. The negative control is named as "Blank B" in the spreasheet and the antibiotic concentrations for each well is defined in column C (Content). - growth_data.xlsx: contains the processed data from "Growth-OD600-Blank_correct.xlsx":growth curves were smoothed with a 5-window moving median and outliers corrected using the filloutliers function in MATLAB. Outliers that were missed were manually corrected. - time_h.xlsx: contains the time in hours used by the matlab function to build the dose response figure S1B. - analysis_code_checkerboard_assay.m: matlab function used to build the dose response figure S1B. Fig-S1C-Bulk_doubling_rates-Bioreactor.zip: - OD600 measurements for each sample in the format "Growth-OD600-treatment-sample_number" (e.g. "Growth-OD600-Ctrl-2.xlsx" refers to no drug control, sample 2). - "Doubl_rate-Bliss_indep-mean.xlsx": contains the mean and standard deviation of doubling rate and bliss independence for the three samples of each treatment (Ctrl, CIP, TET, CIP-TET) as shown in Figure S1C. - "Growth_data-all_samples.xlsx": contains calculations for growth rates, doubling rate, doublig time and Bliss independence for all samples. For more information on methods, strains used and table header descriptions, please refer to the README.txt.

Broughton, J., El Karoui, M., & Fraisse, A. (2024). Cell growth dataset for "Suppression of bacterial cell death underlies the antagonistic interaction between ciprofloxacin and tetracycline in Escherichia coli" [Data set]. Zenodo. https://doi.org/10.5281/zenodo.12685952