A step of bead beating (BioSpec, Bartlesville, OK) for one minute was added to break cells, and all phenol/chloroform/isoamyl alcohol washes were EPZ5676 performed in phase lock gels (5 Prime, Fisher Scientific, Pittsburgh, PA). DNA was removed from extracted RNA with Turbo DNase treatment (Ambion, Austin, TX) at 37°C for 30 min followed

by purification with an RNeasy Mini Kit (Qiagen, Germantown, MD). The quality of RNA was examined by gel electrophoresis using E-gel with SYBR Safer (Invitrogen, Carlsbad, CA). High quality BI 2536 mw RNA was further re-precipitated, concentrated, and stored at -80°C. RNA was reverse transcribed into cDNA using random hexamers (pd(N)6) (GE Healthcare, Piscataway, NJ) and labeled with Amersham CyDye Post-Labeling Reactive Dye (Amersham Biosciences, Piscataway, NJ) following the protocol provided by the Amino Allyl cDNA Labeling Kit (Ambion, Austin, TX). The quantity and labeling efficiency of cDNA was measured using a NanoDrop Spectrophotometer

(ND-1000, TSA HDAC Thermo Scientific, Wilmington, DE). Microarray slides for E. coli were purchased from the University of Alberta (Edmonton, AB, Canada). Each slide contained three replicates of 5,978 70-mer oligonucleotides representing three E. coli strains (4,289 of them were for E. coli K-12). Sample preparation and loading, slide prehybridization, hybridization and washing were performed according to Corning protocols (GAPS II coated slides, Corning Inc., Lowell, MA). An extended 4-h prehybridization using a higher BSA concentration (1 mg/ml) was found to perform best in reducing background noise. Hybridization was in a Corning Microarray Hybridization

Chamber (Corning Inc.) in 42°C water bath. Microarray slides were scanned with a Virtek ChipReader (Virtek Vision, Waterloo, ON, Canada). Spots on scanned images were recognized and pixel intensity for each spot was quantified using Cyclin-dependent kinase 3 the TIGR software Spotfinder (v3.1.1). Gene expression data were analyzed in the software Acuity 4.0 (Molecular Devices, Sunnyvale, CA). LOWESS normalization was performed for every microarray with three iterations using a smoothing factor of 0.4. Hybridized spots with oligonucleotides for strain E. coli K-12 having a high QC (quality control) value (> 0.1), good flag tags (A, B and C) in both Cy3/Cy5 channels were chosen for further analysis. One sample t-tests were performed across replicates. Step-down Bonferroni-Holm was used for the correction of multiple hypotheses testing. Genes with at least two-fold change in expression (p-value < 0.05) were considered to have changed expression during sample dispersion and IMS. Microarray data were deposited in NCBI Gene Expression Omnibus database (GSE22885). Quantitative PCR (qPCR) Primers for qPCR confirmation of the differential expression of eight identified genes in Table 1 are listed in Additional File 2: qPCR primers for nine tested genes.