Figure 1: Experimental setup.
From: The E. coli molecular phenotype under different growth conditions
We performed seven different experiments in which we varied the duration of growth and the temporal density of sampling, the carbon source, and ion concentrations. For each experimental condition, bacteria were grown in three biological replicates. Conditions that are listed multiple times represent independent replicates of those conditions. We subsequently performed whole-transcriptome RNA-Seq for all experimental conditions and mass-spec proteomics for the majority of them. (No proteomics was performed for the low-magnesium experiment.) We considered four different carbon sources: glucose, glycerol, gluconate, and lactate; we also considered high sodium and both low and high magnesium levels. For the time-course and carbon-source experiments, we used base-level Na+ (5 mM) and Mg2+ (0.8 mM) throughout (indicated by [*] in the sodium and magnesium experiments).
