Overview of available gene expression data.

Our study uses a previously published dataset consisting of 155 samples [13, 14]. 152 samples have whole-transcriptome RNA-seq reads and 105 have mass-spec proteomics reads. 102 of the 155 samples have both mRNA and protein reads. Bacteria were grown on four different carbon sources (glucose, glycerol, gluconate, and lactate), two sodium concentrations (base and high), and three magnesium concentrations (low, base, and high). Samples were taken at multiple time points during a two-week interval, and they can be broadly subdivided into exponential phase, stationary phase, and late stationary phase samples.