Supplementary data and scripts for analysis of acid-stress induced LdcI clustering in E. coli

This repository holds a tabular file (S1_file.xlsx) )documenting the data used for data analysis in Kirchner et la.: 

Filamentation-driven peripheral clustering of the inducible lysine decarboxylase is crucial for {E. coli} acid stress response

Page one of the .xlsx file holds statistics on the size and location of clusters detected in WT and 3M E. coli cells after acid-stress induced LdcI production. Data was recorded using dSTORM. Also included is raw data on cell culture growth and medium pH during growth (see Suppl. Fig. 3 in the Manuscript). Page 2 holds data on plasmids, strains and primers used to create the LdcI-3M producing E. coli strain. 

The focal-analyse python script is an all-in-one script which was used to get the statistics from .txt files put out by FOCAL3D (https://github.com/MilsteinLab/FOCAL3D). It can be run in a conda environment set up with the here included environment.yml file to extract and measure cluster sizes, as well as do the distance ratio analysis described in the manuscript (see Methods).