Title of Dataset:
Research data supporting "Indole Pulse Signalling Regulates the Cytoplasmic pH of E. coli in a Memory-Like Manner"
(Scientific Reports, 2019)

Date and location for data collection:
These data were collected in the period between Jan 2017 to December 2019 at the Department of Genetics & Cavendish Laboratory (University of Cambridge, UK).

People responsible for collecting the data:
The data were collected by:
Dr Ashraf Zarkan (University of Cambridge Department of Genetics, email: maa77@cam.ac.uk)
Dr Jinbo Zhu (University of Cambridge, Cavendish Laboratory, email: jc632@cam.ac.uk)
Mr Kareem Al Nahas (University of Cambridge, Cavendish Laboratory, email: ka451@cam.ac.uk)

Contact person for questions:
The contact person for questions regarding the vesicles experiment (Figure 4c) is Mr Kareem Al Nahas.
The contact person for all other experiments is Dr Ashraf Zarkan.

Funding:
Dr Ashraf Zarkan was supported by funding from the was supported by funding from the Leverhulme Trust, UK (RPG-2015-184).
Dr Jinbo Zhu was supported by funding from the UK Engineering and Physical Sciences Research Council (EPSRC, EP/M008258/1).
Mr Kareem Al Nahas was supported by funding from the Winton Programme for the Physics of Sustainability, the Trinity-Henry Barlow Scholarship, the National Physical Laboratory (UK) and an ERC consolidator grant (DesignerPores 647144). 


Data and file overview:

Fig1a.
Data of three biological replicates of E. coli BW25113 WT, showing the cytoplasmic pH (calculated from fluorescence intensity measured by fluorescence spectroscopy) and external pH (measured by pH meter).

Fig1b.
Data of three biological replicates of E. coli BW25113 ∆tnaA, showing the cytoplasmic pH (calculated from fluorescence intensity measured by fluorescence spectroscopy) and external pH (measured by pH meter)

Fig2a.
Data of E. coli BW25113 WT analysed throughout the growth by flowcytometry, showing the statistical analysis of the proportion of cells and the fluorescence intensity of pHluorin and mCherry within each gated population. 
The stats were obtained using FlowJo after defining the gate with a biological control  (E. coli BW25113 WT without pSCM001 plasmid. I.e. with no pHluorin and mCherry fluorescence).

Fig2b.
Data of E. coli BW25113 ∆tnaA  analysed throughout the growth by flowcytometry, showing the statistical analysis of the proportion of cells and the fluorescence intensity of pHluorin and mCherry within each gated population. 
The stats were obtained using FlowJo after defining the gate with a biological control  (E. coli BW25113 ∆tnaA without pSCM001 plasmid. I.e. with no pHluorin and mCherry fluorescence).

Fig3a.
Data of three biological replicates of E. coli BW25113 ∆tnaAwith supplementation of increased concentrations of indole, showing the cytoplasmic pH (calculated from fluorescence intensity measured by fluorescence spectroscopy)

Fig3b.
Data of three biological replicates of E. coli BW25113 ∆tnaAwith a pulse-mimic of indole, CCCP & DNP, showing the cytoplasmic pH (calculated from fluorescence intensity measured by fluorescence spectroscopy)

Fig3c.
Data of three biological replicates of E. coli BW25113 WT grown in LB after removal of the previous indole pulse (by growing overnight in M9/Glucose without tryptophan), showing the cytoplasmic pH (calculated from fluorescence intensity measured by fluorescence spectroscopy)

Fig4a.
Data of three biological replicates of E. coli BW25113 WT & BW25113 ∆tnaA grown in Trizma-buffered LB (pH 8.0), showing the cytoplasmic pH (calculated from fluorescence intensity measured by fluorescence spectroscopy) and external pH (measured by pH meter).

Fig4b.
Data of three biological replicates of E. coli BW25113 WT & BW25113 ∆tnaA grown in Trizma-buffered LB (pH 7.0), showing the cytoplasmic pH (calculated from fluorescence intensity measured by fluorescence spectroscopy) and external pH (measured by pH meter).

Fig4c.
Fluorescence intensity of HPTS dye in large unilamellar vesicles with increased concentrations of indole
Time and intensity was averaged for each concentration of indole and plotted in Fig 4c, with error bars as ±stdev of intensity 

FigS1.
Data of growth curves of E. coli BW25113 WT & ∆tnaA growing for 18 hours in LB or M9/glucose (0.4%)  

FigS3.
Data of three biological replicates of E. coli BW25113 WT & BW25113 ∆tnaA grown in LB, showing the cytoplasmic pH (calculated from means of fluorescence intensity measured by flow cytometry).

FigS4.
Data of three biological replicates showing supernatant indole concentration of E. coli BW25114 WT grown in LB and sampled during lag, exponential and stationary phase
For samples in lag and exponential phase, 50 ml supernatant was passed through C18 column and eluted in 5ml 1-pentanol (a pre-concentration step).
A standard curve of indole was generated using series of 5ml 1-pentanol containing increase indole concentration.


Final Note:
Full description of methods used for data collection and processing can be found in the methodology section of the paper (Scientific Reports - 2019).