Table S1. The results of an over-representation analysis that shows the functional categories that contained significantly more differentially expressed genes than were present in the transcriptome of the indicated treatment. The data is shown for analyses performed separately for each laboratory, indicated as A, B, and C, and for the combined dataset. Functional categories in which the transcripts that were increased were significantly over-represented are indicated by if the q-value < 0.05 or by if the q-value < 0.1. Functional categories in which the transcripts that were decreased were significantly over-represented are indicated by if the q-value < 0.05 or by if the q-value < 0.1. NaCl H2O2 LowFe LowN Epi
Functional category Amino acid metabolism and transport Amino acid metabolism and transport (GABA)
Carbohydrate metabolism and transport Cell division Chaperones/Heat shock proteins Chemosensing & chemotaxis Cofactor metabolism Compatible solute synthesis Cyclic di-GMP cyclase proteins Degradation of xenobiotics Energy generation Fatty acid metabolism Flagellar synthesis and motility Iron metabolism and transport Iron-sulfur proteins Light and oxygen sensing LPS synthesis and transport Mechanosensitive ion channel Nitrogen metabolism Nucleotide metabolism and transport Organic acid metabolism and transport Outer membrane proteins Oxidative stress tolerance Oxidative stress tolerance (Antioxidant enzymes)
Peptidoglycan/cell wall polymers Phage & IS elements Phosphate metabolism and transport Phospholipid metabolism Phytotoxin synthesis and transport Pili synthesis and regulation Polyamine metabolism and transport Polysaccharide synthesis and regulation Post-translational modification Proteases QAC metabolism and transport Replication and DNA repair
Apo
NaCl H2O2 LowFe LowN Epi Apo
ABCABCABCABCABCABC
Combined dataset
Table S1 (continued) The genes were each assigned to a single functional category and were identified as differentially expressed by the treatment if the False discovery rate was 0.01).
