BioRDM : Biological Research Data Management
Published April 30, 2024 | Version v2
Dataset Open

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

Creators

  • 1. ROR icon University of Edinburgh

Contributors

Data curator:

  • 1. ROR icon University of Edinburgh

Description

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, intermediate and slow growth (M9 based medium supplemented with: glucose and amino acid, glucose, and glycerol, respectively).
Two types of assays were performed: a checkerboard assay with a 2-dimension gradient of antibiotic concentrations shown in "Fig-S1-Growth_rates-Checkerboard_assay.zip", and bulk growth rates assay  shown in "Fig-S2-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-S1-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-S2-Bulk_doubling_rates-Bioreactor.zip:

- "bulk_doubling rates_gly/glu/gluaa.csv": contains the calculated doubling rates for each of three experimental replicates (rows) and for each antibiotic treatment (columns: Ctrl, CIP, TET, CIP-TET) as shown in Figure S2. These values were used to calculated the Bliss independence (for further details see https://gitlab.com/MEKlab/single-cell-suppression-2024/figure plotting.ipynb
   - Folders containing OD600 measurements and calculated growth rates for each growth medium, which are further separated into folders for each experimental replicate. Each replicate folder is labelled as the date the experiment was performed (denoted as "*" hereon). Each contains the following: raw optical density data (*.txt files), summary of experiment and results (*.docx file), the function compute_growth_rates.m, and the script Growth_curves_*.m.

For more information on methods, strains used and table header descriptions, please refer to the README.txt. 

Files

README.txt

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md5:dba39bc131f6d8c40d8565b77f38239f
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Additional details

Related works

Is published in
Preprint: 10.1101/2024.04.18.590101 (DOI)

Funding

Wellcome Trust
DNA repair and genetic stability: Elucidating the effects of cell physiology in Escherichia coli 205008/Z/16/Z
UK Research and Innovation
UKRI Centre for Doctoral Training in Biomedical Artificial Intelligence EP/S02431X/1