Growing pains: natural stress response during growth of B. subtilis (high density time-resolved transcriptome analysis)

We have determined the time-resolved transcriptome of the model gram-positive organism B. subtilis during growth on rich medium. DNA microarrays were used to monitor gene transcription in 10-minute intervals at 40 consecutive timepoints. From the growth curve and a PCA analysis of all gene expression levels, we identified 4 distinct growth phases: a lag phase, an exponential growth phase, and very clearly separated early and late stationary growth phases For each time point, labeled cDNA was hybridized to a microarray slide together with labeled cDNA from the previous timepoint. In addition, the same DNA was used in a dye swap hybridization with the labeled cDNA from the subsequent timepoint. Lastly, labeled cDNA from each timepoint was hybridized with labeled cDNA from 30 mins later (e.g., 1 vs 4, 2 vs 5 etc.). The three slides resulted in six measurements per gene, since each slide contains two duplicate spots for all genes. Duplicate spots on the same array were analyzed separately, for a total of 118 Samples from the 56 hybridizations. Therefore, the same raw data file is associated with the '#1' and '#2' sample of a given comparison (eg. GSM495251 and GSM495252).