Expression Data Set 54 details

Information Item Value
Dataset Name Affymetrix chips for chloramphenicol induction
Dataset Number 54
Short Description Affymetrix Expression Experiments showing effect of induction by chloramphenicol.
Source URL
Reference Cheung, KJ, Badarinarayana,V, Selinger, D, Janse, D, and Church, GM (2002)A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli. Genome Research Feb;13(2):206-15.
Strains NONE
Conditions Contains replicates of two samples: 0 timepoint and 40 minutes
post induction with chloramphenicol, plus a single sample 10 minutes post induction with chloramphenicol.
Date Added to ExpressDB Aug 8 2001 2:48:09:860PM
Number of Measures on ExpressDB 60 (here to download dataset and view measure details)
Long Description Changes in DNA supercoiling are induced by a wide range of environmental stresses in Escherichia coli, but the physiological significance of these responses remains unclear. We now demonstrate that an increase in negative supercoiling is necessary for transcriptional activation of a large subset of osmotic stress response genes. Using a microarray-based approach, we have characterized supercoiling-dependent gene transcription by expression profiling under conditions of high salt, in conjunction with microbial antibiotics novobiocin, pefloxacin, and chloramphenicol. Algorithmic clustering and statistical measures for gauging cellular function show that this subset is enriched for genes critical in osmoprotectant transport/synthesis and rpoS-driven stationary phase adaptation. Transcription factor binding site analysis also supports regulation by the global stress sigma factor rpoS. In addition, these studies implicate 60 uncharacterized genes in the osmotic stress regulon, and offer evidence for a broader role for supercoiling in the control of stress-induced transcription.
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