ArticleScientific reports2017
The E. coli molecular phenotype under different growth conditions.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Bacterial stress responses lower mRNA-protein level correlations.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Maintenance of cytoplasmic and membrane densities shapes cellular geometry in Escherichia coli.Nature communications · 2025Article
- Propensity for proto-gene emergence in bacteria.Genome biology · 2025Article
- Article
- De novo gene birth and the conundrum of ORFan genes in bacteria.Genome research · 2025Review
- The microbiologist's guide to metaproteomics.iMeta · 2025Review
- Bacterial extracellular vesicles target different bacterial species, impairing cell division and diminishing their pathogenicity.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Genetic properties underlying transcriptional variability across different perturbations.Nature communications · 2025Article
- Towards improved biofilm models.Nature reviews. Microbiology · 2025Review
- L-Rhamnose Globally Changes the Transcriptome of Planktonic and BiofilmMicroorganisms · 2024Article
- Analysis of bacterial transcriptome and epitranscriptome using nanopore direct RNA sequencing.Nucleic acids research · 2024Article
- 'Wild Type'.Microbiology (Reading, England) · 2024Review
- Promoter recruitment drives the emergence of proto-genes in a long-term evolution experiment with Escherichia coli.PLoS biology · 2024Article
- Creating Polyploid Escherichia Coli and Its Application in Efficient L-Threonine Production.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- System-wide optimization of an orthogonal translation system with enhanced biological tolerance.Molecular systems biology · 2023Article
- Engineering tRNA abundances for synthetic cellular systems.Nature communications · 2023Article
- A Stenotrophomonas maltophilia TetR-Like Transcriptional Regulator Involved in Fatty Acid Metabolism Is Controlled by Quorum Sensing Signals.Applied and environmental microbiology · 2023Article
- Article
- About the dark corners in the gene function space of Escherichia coli remaining without illumination by scientific literature.Biology direct · 2023Article
- The RNA repair proteins RtcAB regulate transcription activator RtcR via its CRISPR-associated Rossmann fold domain.iScience · 2022Article
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
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. Additionally, we provide measurements of doubling times and in-vivo metabolic fluxes through the central carbon metabolism. 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.
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