DOI: 10.5281/zenodo.15088910
title: Protein aggregation dynamics in aging Escherichia coli

description: Summary

Single-cell microscopy data of Escherichia coli cells expressing DnaK chaperones labeled with msfGFP. Cells were grown in mother machine microfluidic devices for 48h at 37°C in M9 minimal medium, with phase constrast images acquired in 2min intervals and fluorescence images in 10min intervals. These images were processed using the DeLTA (Deep Learning for Time-lapse Analysis) pipeline, and the resulting data was post-processed with a custom R program to correct segmentation errors. For each cell lineage, we tracked a mother cell over ~60 generations, and its daughters from birth to the first cell division (1 generation). 

 

File descriptions

DnaK_allsibs_share.rds: Data refers to E. coli MG1655 expressing DnaK-msfGFP, and consists of list of two data frames, where the first contains information on mother cells and the second on daughters. Each line represents a generation, and is paired up between the two data frames.



well: Maternal lineage identification

id: Cell division id (indicates generations)

time.of.birth: Time of first frame after cell division, in hours 

len.at.birth: Cell length after division, in pixels

len.at.div: Cell length before division, in pixels

fluo1.at.birth: Mean DnaK-msfGFP fluorescence (arbitrary units)

r: Elongation rates (per minute) over each generation

divint: Division intervals over each generation (in minutes)

age: 0 for mothers, 1 for daughters

agg.length: Diameter of protein aggregate, if present (in pixels)

agg.f1mean: Mean fluorescence of protein aggregate, if present (arbitrary units)

agg.relativelength: Relative size of aggregate (ratio between agg.length and len.at.birth)

agg.disp: For cells containing aggregates, estimate of dispersed (non-aggregated) fluorescence (arbitrary units)

has.agg: T/F, whether or not an aggregate has been detected in a given generation


 

WT_allsibs_share.rds: Data refers to MG1655 E. coli, and consists of a list of two data frames, where the first contains information on mother cells and the second on daughters. Each line represents a generation, and is paired up between the two data frames.



well: Maternal lineage identification

id: Cell division id (indicates generations)

time.of.birth: Time of first frame after cell division, in hours 

len.at.birth: Cell length after division, in pixels

len.at.div: Cell length before division, in pixels

fluo1.at.birth: Mean DnaK-msfGFP fluorescence (arbitrary units)

r: Elongation rates (per minute) over each generation

divint: Division intervals over each generation (in minutes)

age: 0 for mothers, 1 for daughters


 

DnaK_transects: Data refers to E. coli MG1655 expressing DnaK-msfGFP, and consists of a list of two matrices, where the first contains information on mother cells and the second on daughters. Each line represents a generation, and is paired up between the two data frames. The rows are also paired with those of DnaK_allsibs_share.rds. Each row contains fluorescence measurements of every pixel across the long axis of each cell, from old pole to new pole, shortly after cell division.R scripts: Each script contains the necessary R code to reproduce the plots and statistical analyses of figures in the associated manuscript, using the three datasets provided.