RT Journal Article SR Electronic T1 The E. coli molecular phenotype under different growth conditions JF bioRxiv FD Cold Spring Harbor Laboratory SP 082032 DO 10.1101/082032 A1 Mehmet U. Caglar A1 John R. Houser A1 Craig S. Barnhart A1 Daniel R. Boutz A1 Sean M. Carroll A1 Aurko Dasgupta A1 Walter F. Lenoir A1 Bartram L. Smith A1 Viswanadham Sridhara A1 Dariya K. Sydykova A1 Drew Vander Wood A1 Christopher J. Marx A1 Edward M. Marcotte A1 Jeffrey E. Barrick A1 Claus O. Wilke YR 2016 UL http://biorxiv.org/content/early/2016/10/23/082032.abstract AB Modern systems biology requires extensive, carefully curated measurements of cellular components in response to different environmental conditions. While high-throughput methods have made transcriptomics and proteomics datasets widely accessible and relatively economical to generate, systematic measurements of both mRNA and protein abundances under a wide range of different conditions are still relatively rare. Here we present a detailed, genome-wide transcriptomics and proteomics dataset of E. coli grown under 34 different conditions. We manipulate concentrations of sodium and magnesium in the growth media, and we consider four different carbon sources glucose, gluconate, lactate, and glycerol. Moreover, samples are taken both in exponential and stationary phase, and we include two extensive time-courses, with multiple samples taken between 3 hours and 2 weeks. We find that exponential-phase samples systematically differ from stationary-phase samples, in particular at the level of mRNA. Regulatory responses to different carbon sources or salt stresses are more moderate, but we find numerous differentially expressed genes for growth on gluconate and under salt and magnesium stress. Our data set provides a rich resource for future computational modeling of E. coli gene regulation, transcription, and translation.