Discovery of transcription factor and regulatory network function through systematic deletion and quantitative phenotyping analysis in archaea

Halobacterium salinarum ∆cspD1 transcription factor deletion mutant and control strain NRC-1 of Halobacterium salinarum were grown to mid-logarithmic phase in batch mode in a New Brunswick BioFlo100 modular bench top fermentor (New Brunswick Scientific) in CM medium as described in (Schmid et al., 2007, Genome Res, 17(10):1399-413. At mid-log phase, oxygen sparging and agitation were stopped to induce anoxia. Cultures were incubated anaerobically overnight, then oxygen was sparged and RNA was collected at time points immediately prior to addition of oxygen and 5, 10, 20, 45, and 180 minutes afterwards. Although these data were published previously as part of a larger gene regulatory network study (Brooks et al., 2014, Mol Sys Biol, 10:740), the details of the experiment and specific analysis of the effect of ∆cspD1 deletion on gene expression were not reported. 6 samples from conditions of varying oxygen tension from strain delta-cspD1 were hybridized against RNA from wild type control NRC-1 strain (RNA batch d) on dye-swap arrays (replicates) for a total of 12 arrays.