The absence of contaminating DNA and the quality of the RNA was confirmed by the lack of PCR amplification of known genes (i.e.: fnr) and by using agarose-gel electrophoresis. Aliquots of the RNA samples were kept at -80°C for use in the microarray and the qRT-PCR studies. Microarray studies S. Typhimurium microarray slides were prepared and used as previously described Selleckchem IWR-1 [24]. For the hybridizations, the SuperScript™ Indirect cDNA Labeling System (Invitrogen) was used to synthesize the cDNA from the RNA prepared from the WT and arcA mutant strains. Dye swapping was performed to avoid dye-associated effects on cDNA

synthesis. Slide hybridizations and scanning were carried-out using the same protocols and equipment as previously described [20]. Data analysis Cy3 and Cy5 values for each spot were normalized over the total intensity for each dye, to account for differences in total intensity between the two scanned images. The consistency of the data obtained from the microarray analysis was evaluated using two methods: (i) a pair-wise comparison, calculated with a two-tailed Student’s t test and analyzed by the MEAN and TTEST procedures of SAS-STAT this website statistical software (SAS Institute, Cary, NC) [the effective degrees of freedom for the t test were calculated as previously described [25]; and (ii) a regularized t test followed by a posterior probability of differential expression [PPDE Temsirolimus ic50 (p)] method. The signal

intensity at each spot from the arcA mutant and the WT were background-subtracted, normalized, and used to calculate the ratio of gene expression

between the two strains. All replicas were combined and the median expression ratio and standard deviations calculated for ORFs showing ≥ 2.5-fold change. Microarray data The microarray data are accessible via GEO Accession Number GSE24564 at http://​www.​ncbi.​nlm.​nih.​gov/​geo/​query/​acc.​cgi?​acc=​GSE24564. qRT-PCR qRT-PCR [26] was used to validate the microarray data [27]. Seventeen genes were randomly PJ34 HCl chosen (Table 2) from the differentially expressed genes. Primers (Integrated DNA Technologies, Coralville, IA) were designed and qRT-PCRs were carried-out using QuantiTectTM SYBR® Green RT-PCR Kit (Qiagen), an iCycler™ (Bio-Rad, Hercules, CA), and the data were analyzed by the Bio-Rad Optical System Software – Version 3.1, according to the manufacturer specifications. The cycling conditions comprised 30 min of a reverse transcriptase reaction at 50°C, 15 min of polymerase inactivation at 95°C, and 40 cycles each of 94°C for 15 sec for melting, 51°C for 30 sec for annealing, and 72°C for 30 sec for extension followed by 31 cycles each at 65°C for 10 sec to obtain the melt curve. To ensure accurate quantification of the mRNA levels, three amplifications of each gene were made using 1:5:25 dilutions of the total RNA. Measured mRNA levels were normalized to the mRNA levels of the housekeeping gene, rpoD (σ70).