DOI: 10.5061/dryad.7d7wm3845
title: Data from: A link between aging and persistence

description: This dataset was used to establish a connection between two phenomena
 related to phenotypic heterogeneity in bacteria: antibiotic persistence
 and aging. It contains physiological measurements of Escherichia
 coli cells growing within microfluidic devices, in either exponential or
 stationary phase. Populations growing exponentially were subjected to
 damaging treatments, either through photo-oxidation of sub-inhibitory
 Streptomycin concentrations, or to persistence triggering via Tetracycline
 exposure. Only the latter treatment produced persisters during exponential
 phase. Data from stationary phase populations includes the transition from
 exponential to stationary phase, showing that cells inheriting old poles
 arrest growth earlier than those inheriting new poles.
description: <em>Escherichia coli </em>cells were grown in mother
 machine and dial-a-wave microfluidic devices, and imaged through
 time-lapse microscopy. Cell segmentation was performed on ImageJ to
 determine cell sizes, elongation rates, and doubling times. The area of
 protein aggregates was determined with MicrobeJ.
description: # Data from: A link between aging and persistence
 [https://doi.org/10.5061/dryad.7d7wm3845](https://doi.org/10.5061/dryad.7d7wm3845) ## Description of the data and file structure Data on *Escherichia coli* elongation rates, doubling times, and survival over time were obtained by culturing populations in microfluidic devices. All populations were grown in LB media at 37°C. Cell segmentation and tracking was performed on ImageJ. ### Files and variables #### File: Data\_for\_Fig\_2A.csv **Description:** Growth over time for bacteria growing in continuous exponential phase in mother machine microfluidic devices. ##### Variables * Time (hours): time of birth, recorded immediately after cell division. * Elongation.rate (min-1): rate of length elongation for a given cell, measured between birth and division. Data is normalized by population means. * Age (categorical): 0 = old daughter, 1 = new daughter #### File: Data\_for\_Fig\_2B.csv **Description:** Doubling times of mother and daughter cells in consecutive generations, for bacteria growing in continuous exponential phase in mother machine microfluidic devices. ##### Variables * mother (min): normalized maternal doubling times. * daughter (min): normalized daughter doubling times. * daughter.age (categorical): Age of the daughter cell. 0 = old daughter, 1 = new daughter #### File: Data\_for\_Fig\_2D.csv **Description:** Growth over time for bacteria growing in continuous exponential phase in dial-a-wave devices, in unstressed conditions for 9 h, followed by exposure to 100 µg/ml Ampicilin. ##### Variables * time.of.birth (hours): time at which a given generation starts, right after cell division. * time.of.division (hours): time at which a given generation end, right before cell division. * r (min-1): elongation rates * age (categorical): 0 = old daughter, 1 = new daughter #### File: Data\_for\_Fig\_3A.csv **Description:** Growth over time for bacteria growing in continuous exponential phase in mother machine microfluidic devices. Cells were grown under photo-oxidative treatment, followed by Streptomycin exposure. ##### Variables * time.of.birth (hours): time at which a given generation starts, right after cell division. * time.of.division (hours): time at which a given generation end, right before cell division. * r (min-1): elongation rates * age (categorical): 0 = old daughter, 1 = new daughter #### File: Data\_for\_Fig\_3B.csv **Description:** Growth over time for bacteria growing in continuous exponential phase in mother machine microfluidic devices. Cells were grown under sub-inhibitory Streptomycin treatment, followed by Nalidixic Acid exposure. ##### Variables * time.of.birth (hours): time at which a given generation starts, right after cell division. * time.of.division (hours): time at which a given generation end, right before cell division. * r (min-1): elongation rates * age (categorical): 0 = old daughter, 1 = new daughter #### File: Data\_for\_Fig\_3C.csv **Description:** Growth over time for bacteria growing in continuous exponential phase in mother machine microfluidic devices. Cells were exposed to a bacteriostatic Tetracycline treatment for 30 min, followed by Ampicillin exposure and subsequent recovery. ##### Variables * time.of.birth (hours): time at which a given generation starts, right after cell division. * time.of.division (hours): time at which a given generation end, right before cell division. * r (min-1): elongation rates * age (categorical): 0 = old daughter, 1 = new daughter #### File: Data\_for\_Fig\_4A.xlsx **Description:** Bacteria grown in microfluidic devices. Populations were initially maintained in exponential phase, then transitioned to stationary phase through a gradual dilution of the culture media with spent medium. After 24h, cells were treated with Ampicillin. Persister cells were observed upon recovery. ##### Variables * Time.of.birth (hours): time at which a given generation starts, right after cell division. * Time.of.division (hours): time at which a given generation end, right before cell division. * Elongation rates (min-1): elongation rates * Age (categorical): 0 = old daughter, 1 = new daughter #### File: Data\_for\_Fig\_4C.xlsx **Description:** Doubling times of mother and daughter cells in consecutive generations, for bacteria transitioning between exponential and stationary phase within mother machine microfluidic devices. ##### Variables * Maternal doubling time (min): doubling time of the mother cell * New daughter (min): doubling time of the daughter cell inheriting a maternal new pole * Old daughter (min): doubling time of the daughter cell inheriting a maternal old pole * Phase (categorical): Exponential or Stationary #### File: Data\_for\_Fig\_5AB.csv **Description:** Size of bacteria protein aggregates, measured on strains expressing IbpA-YFP in agarose pads with or without Streptomycin. ##### Variables * strep: 0µg/ml or 1µg/ml Streptomycin * aggregate.area (px): area of the IbpA-YFP fluorescent foci * relative.aggregate.area: ratio between the area of the IbpA-YFP fluorescent foci and the cell area #### File: Data\_for\_Fig\_S3B.xlsx **Description:** Bacterial growth over time in dial-a-wave microfluidic devices. ##### Variables * Time.of.birth (hours): time at which a given generation starts, right after cell division. * Time.of.division (hours): time at which a given generation end, right before cell division. * Elongation.rates (min-1): elongation rates * Age (categorical): 0 = old daughter, 1 = new daughter * Strain (categorical): *E. coli* MG1655 WT (wildtype) or *hipA7* #### File: Data\_for\_Fig\_S3A.xlsx **Description:** Bacterial doubling times in dial-a-wave microfluidic devices. ##### Variables * Maternal doubling time (min): doubling time of the mother cell  * New daughter (min): doubling time of the daughter cell inheriting a maternal new pole * Old daughter (min): doubling time of the daughter cell inheriting a maternal old pole * Strain (categorical): *E. coli* MG1655 WT (wildtype) or *hipA7* ### Note on NA variables For all files listed above, measurements of elongation rates and/or doubling times were only recorded when a given cell could be followed from birth to division (a complete generation). For example, if a cell did not divide until the end of the imaging period, its doubling time is unkown (=NA). If a cell entered or exited the imaging field at an unkown timepoint of its cell cycle, its doubling time is NA. Similarly, the age of a cell can only be known after we have followed the lineage for at least two consecutive divisions, and therefore the age of the first cell in the lineage is unknown (=NA).