Analysis of microarray images was carried out applying the ImaGene 6.0 software (BioDiscovery) as described previously [42]. Lowess normalization and significance test (fdr) were performed with the EMMA software [60]. M-values (log2 experiment/control ratio), P-values (t test) and A-values were also calculated with EMMA. The M-value represents the logarithmic ratio between both channels. The A-value represents the logarithm of the combined intensities of both channels. The microarray Caspase inhibitor results were verified for specific genes
by quantitative reverse transcription-PCR using a QuantiTect SYBR Green reverse transcription-PCR kit (QIAGEN, Hildesheim, Germany) according to the manufacturer’s instructions. Filtering find more and clustering analysis of the microarray data K-means
clustering analysis of the microarray time-course data was performed with the aid of the Genesis software [62]. After normalization, only genes with approximately threefold change in expression (M-value of ≥ 1.4 or ≤ -1.4) in at least one point of time in the wild type microarrays were considered for clustering analysis. Genes that did not present an evaluable expression value for at least 5 of the 6 points of time (missing values on the microarray flagged as empty spots) were not considered. K-means clustering was used for distributing differentially regulated genes into 6 groups, both with the wild type and with the rpoH1 mutant microarray data. Quantitative RT-PCR analyses Reverse transcription
was performed using Superscript II reverse transcriptase (Invitrogen) with random hexamers as primers. RNA samples were tested for two time points, 10 and 60 minutes after pH shock. Real-time PCRs were run on an Opticon system (BioRad) using the FastStart DNA MasterPLUS SYBRGreen I kit (Roche) according to the manufacturer’s instructions. The housekeeping gene rkpK was used as a reference for normalization. The sequences of the primers used are available at http://www.cebitec.uni-bielefeld.de/groups/brf/software/gendb_info/. Three independent cultures were analyzed, as GPX6 well as three technical replicates, for each time point. Microarray data accession numbers The entire set of microarray data has been deposited in the ArrayLims database [63]. Acknowledgements We thank Victoria Gödde, Manuela Meyer and Eva Schulte-Berndt for providing outstanding technical help. This work was supported by a scholarship from the NRW Graduate School in Bioinformatics and Genome Research, funded by the Ministry of Innovation, Science, Research and Technology of the state of North Rhine-Westphalia, Germany. Electronic supplementary material Additional file 1: Complementation of rpoH1 mutation.