The data and MATLAB and Python code used for analysis and figure generation of E. coli pulsing/starvation project is provided here. All the MATLAB code was written in version 2015b.
This Github is divided as follows:
- Part 1 - Data and analysis of lag time versus feeding frequency - contains all of the OD data and code used for the wild-type pulsing experiments. Code generates the following plots:
- All OD versus time plots with linear threshold fitting
- Lag time versus feedrate
- Feedrate versus linear growth rate
- Total glucose needed for proliferation versus feedrate
- Summary table
- Part 2 - Flow Cytometry data and analysis. Code compares counts versus OD. Flow cytometry data is available from https://doi.org/10.5281/zenodo.1035825
- Part 3 - Microscopy measurement data and analysis.
- Part 4 - Ion data data and analysis for varying feedrates. Code parses the ion data and generates plots where feedrate is varied (0.06, 0.12, 0.18 mmol/g/h) with the negative control in the background (f = 0 mmol/g/h)
- Part 5 - Ion data data and analysis for antibiotic additions. Code parses the ion data and generates plots where f = 0.18 mmol/g/h and antibiotics (Chloramphenicol, Rifamycin, and AZT) are added.
- Part 6 - Code to find intersecting proteins amongst those involved in division and that are degraded.
- Part 7 - Data and code for perturbing lag time (e.g. protease inhibitor, FtsZ titration)
- Part 8 - Data and code for Crp and PdhR KO pulsing experiments.
- Part 9 - FtsZ modeling code. Code used to generate and test the FtsZ model (numerical and analytical solution).
- Part 10 - Microfluidic data analysis. Code generates the cumulative fraction curves, GFP/cell over time, and length/cell over time.
- Part 11 - Code used to generating labeling fraction figure.
- Common - contains common functions used throughout the different parts.