Transcriptional response of Escherichia coli O157 TUV93-0 to small molecule inhibitors of TTS

The transcriptional profile of Escherichia coli O157 treated with small molecule inhibitors of type III secretion was determined. Four variations of the small molecule inhibitor were assessed for global changes in transcription by treating cells with 20uM of inhibitor or an equivalent volume of DMSO (inhibitor solvent). Keywords: treatment, dose, Cy3, Cy5, 2-colour For each inhibitor, biological tripicates of treated (20uM inhibitor in DMSO) and untreated (DMSO only) cultures were grown in 25ml of MEM-HEPES supplemented with 0.1% Glucose and 250nM Fe(NO3)2. RNA was extracted from 15ml of culture at OD 0.7 and labeled with Cy5 (treated) and Cy3 (untreated) (excepting ME0055 that was performed as a dye swap). Labeled untreated RNA was pooled prior to hybridisation. Treated RNA (biological replicates) and pooled untreated RNA was hybridised to microarray slides. Slides were scanned using an Axon 4100A scanner and data processed using Genespring GX.