High-throughput identification of transcription start sites , conserved promoter motifs , and regulons

Caulobacter cell cycle time series. Swarmer cells were isolated using standard procedures and allowed to proceed through the cell cycle (150 minutes in these conditions) in minimal media (M2G). Samples were taken every 12 minutes for 156 minutes. RNA was extracted from each sample, reverse transcribed into cDNA, fractionated, labeled, and then hybridized onto the Caulobacter array using the method of Lizewski et al.. The 72 minute time point assay failed. After scanning and normalizing the intragene probe signals from the CauloHI1 arrays, we generated a time series of expression for each gene by averaging the difference between perfect match and mismatch of each probe pair within a gene after discarding outliers. Outliers were defined as probe pairs with an average expression less than zero or greater than three standard deviations from the other intragene probe pairs. Prior to this averaging, probe pairs within 25 bp of each other were averaged together to prevent over sampling of either end of the gene. The cell cycle data set from the chips for the 13 time points (excluding the 72 min point) is in Table T8 online at startsite.