Planktonic and biofilm cells were grown as described above in flasks (for planktonic) or in bovine-serum coated 6 well plates (for biofilms). Biofilm cells were harvested with a sterile transfer pipet, biofilm or planktonic cells were centrifuged at 3,000 × g for 5 min, supernatant was removed and cell pellets were frozen in liquid nitrogen and stored at −80°C. Total RNA was extracted using the Ambion RiboPure-Yeast RNA kit (AM1926) according to the manufacturer’s protocol. Synthesis of cDNA and dye coupling was performed as described in (Nobile et al., 2009 (link)). Gene expression microarrays from Agilent Technologies (AMID #020166), were used as described in (Nobile et al., 2012 (link)). LOWESS normalization of microarray data was performed as previously described (Lohse and Johnson, 2010 (link)). At least two independent replicates were performed at each timepoint. Microarray data is reported in Dataset 1 and raw gene expression array data is stored at the Gene Expression Omnibus (www.ncbi.nlm.nih.gov/geo, accession #GSE61143).