To study the changes in gene expression after DNA damage in E. coli we used whole-genome gene arrays, containing all the annotated ORFs of E. coli. Bacterial cultures were grown to early- to mid-log phase and mitomycin C (MMC) was added to the growth media. Samples at several time points after induction of DNA damage were taken and total RNAs were purified from them. Radiolabeled probes were generated by reverse transcription of purified RNAs with a mixture of all the gene-specific oligonucleotides used as primers. Following purification, the probes were hybridized to gene arrays. In each experiment we compared the levels of expression of genes after the induction of DNA damage with their expression level before damage.
