The GSEA parameters used included: Pearson metric and gene set size restrictions, 10 minimum, 500 maximum. Gene sets significantly modified

by fosfomycin treatment were identified using a multiple hypothesis testing FDR < 0.25. GSEA see more was performed for each time point (10, 20 and 40 min) at which gene expression was correlated with fosfomycin concentration. Positive correlation was interpreted as up-regulation of a gene set resulting from drug treatment; a negative correlation was interpreted as down-regulation. Meta-analysis: integration of gene expression data from other sources Our experimental data was compared to other publicly available S.

aureus transcriptomic data. To ease the comparison, the recently published “”Staphylococcus aureus microarray meta-database”" (SAMMD) was used [3]. The qualitative transcriptional profiles (up or downregulation) were coupled with the quantitative transcriptional profile of fosfomycin to a single spreadsheet (Additional file 1) in order to analyze the similarities and differences between different Fedratinib research buy responses. Quantitative real-time PCR (qPCR) The purified RNA samples from experimental points t40c0, t40c1 and t40c4 were reverse transcribed using High Capacity cDNA Reverse Transcription Kit (Applied Biosystems). The acquired cDNA was used to validate the microarray differential expression for genes listed in Table 3. All qPCR reactions were performed on a LightCycler LC480 Detection System (Roche) in 384-well plate format using universal cycling conditions (2 min at 50°C, 10 min at 95°C,

followed by 50 cycles of 15 s at 95°C and 1 min at 60°C). Real-time PCR was performed in a final reaction volume of 5 μL containing 2 μL of diluted cDNA sample, 1× primer-probe mix (TaqMan® Gene Expression Assay, Applied Biosystems) and 1× TaqMan® Universal PCR Master Mix (Applied Biosystems). Each sample cDNA was tested for five target genes: atl, murZ, oppB, ribB, isometheptene sgtB and the endogenous control 16S rRNA [32]. The TaqMan® chemistry based primers and probes were designed and synthesized by Applied Biosystems (Table 3). Each reaction was performed in two replicate wells in two dilutions on the same 384-well plate. An automated liquid handling system (Multiprobe® II plus ex, PerkinElmer) was used to prepare cDNA dilutions, to pipette cDNA samples and master mixes onto the 384-well plates. Table 3 Primer and probe sequences used for qPCR analysis.