Time series (T= 0-4 hours) for E. coli K-12 MC4100 after a shift from 23˚C to 37˚C (M9 minimal glycerol medium, exponential phase growth)
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PROVIDER: PRJNA697923 | ENA |
REPOSITORIES: ENA
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Project description:The aim of this study is to investigate the changes of global gene expression in E. coli during a carbon source shift. Expression profiling of an evolved strain of E. coli K12 MG1655 grown in M9 minimal media supplemented with propylene glycol or glycerol.
2012-06-01 | GSE34631 | GEO
Project description:The aim of this study is to investigate the changes of global gene expression in E. coli during a carbon source shift. Expression profiling of an evolved strain of E. coli K12 MG1655 grown in M9 minimal media supplemented with propylene glycol or glycerol. A six chip study under two separate culture conditions
2012-05-31 | E-GEOD-34631 | biostudies-arrayexpress
Project description:We investigated the effect of a temperature shift from 23˚C to 37˚C, mimicking the temperature transition experienced by a microbe as it enters a human host. This strategy allowed the exploration of the kinetics of gene expression changes in immediate response to a temperature upshift and to characterize the suite of genes required to respond to 37˚C in the first few hours. We demonstrate that a significant number of genes are rapidly altered in expression within minutes to hours after a temperature shift. Some are only induced transiently, while are required for long-term adaptation. Many of these genes are related to metabolism, stress response, and immune evasion suggesting that temperature may serve as a sentinel cue to predict and prepare for niche adaptation in the host.
2021-09-19 | GSE165794 | GEO
Project description:Because many virulence genes in E. coli and other pathogens are regulated by temperature, we wanted to determine on a genome-wide scale which genes are modulated in adapting to both human host temperature (37˚C) and ambient room temperature (23˚C). Overall, 126 genes were found to be more highly expressed at 37˚C (1) whereas 297 genes were more highly expressed at 23˚C (2). Genes involved in the uptake and utilization of amino acids, carbohydrates, and iron dominated the 37˚C list, supporting a model in which temperature serves as a host cue to increase expression of bacterial genes needed for growth. 122 of the 297 genes more highly expressed at 23˚C are RpoS-controlled, confirming genome-wide the model that low temperature serves as a primary cue to trigger the general stress response. Several genes expressed at 23˚C overlap with the cold shock response, suggesting that strategies used to adapt to sudden shifts in temperature also mediate long-term growth at 23˚C. Another category of genes more highly expressed at 23˚C are associated with biofilm development, implicating temperature as an important cue influencing this developmental pathway. 1.) White-Ziegler, C. A., A. J. Malhowski, and S. D. Young. Human body temperature (37˚C) increases the expression of iron, carbohydrate, and amino acid utilization genes in Escherichia coli K-12. Journal of Bacteriology 2007. Vol. 189(15):5429-40. Epub 2007 May 25. 2.)White-Ziegler, C. A., S. Um, N.Peréz, A. L. Berns, A. J. Malhowski, and S. Young. Biofilm, coldshock, and RpoS-dependent genes demonstrate increased expression during low temperature growth (23˚C) in Escherichia coli K-12. In revision for Microbiology. Keywords: stress response
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Project description:Growth to mid exponential phase in M9 minimal media supplemented with 0.5% lactate versus growth in rich LB media Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Media: M9 minimal media with 0.5% lactate Keywords: Logical Set
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Project description:A proteome and acetylome study under different culture conditions was carried out by quantitative label-free mass spectrometry analysis. E. coli K12 BW25113 strain was grown employing TB7 complex medium or M9 minimal medium, supplemented with glucose 20 mM or glycerol 40 mM as carbon source. Therefore, 4 culture conditions (TB7-glucose, TB7-glycerol, MM9-glucose, and MM9-glycerol) were used. Samples were taken in exponential and in stationary growth phase, resulting in 8 experimental samples: TB7-glucose in exponential phase, TB7-glucose in stationary phase, TB7-glycerol in exponential phase, TB7-glycerol in stationary phase, MM9-glucose in exponential phase, MM9-glucose in stationary phase, MM9-glycerol in exponential phase, and MM9-glycerol in stationary phase, with 4 biological replicates from each. This work emphasises the importance of the culture conditions choice, as they determine both, location of acetylation, and acetylation level, which may have an impact on regulation of the central metabolism.
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Project description:Gene expression in E.coli K-12 MC4100 at 37°C and 23°C in M9 glycerol exponential phase growth
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Project description:Laboratory adaptive evolution experiments were conducted using serial passage of E. coli in M9 minimal medium supplemented with either 2 g/L of lactate for 60 days or 2 g/L of glycerol for 44 days. 7 parallel evolution strains were generated for growth on lactate and 7 parallel evolution strains were generated for growth on glycerol. Affymetrix arrays were used to study the time-course change in gene expression from unevolved E. coli (day 0) to a midpoint evolved strain (day 20) and evolutionary endpoints
2011-10-22 | GSE33147 | GEO
Project description:Study of the possible existence of a replication fork trap in Vibrio cholerae. 1- FX85: EPV50(WT) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 2- FX86: EPV50(WT) grown in M9 minimal medium supplemented with 0.4 % fructose to stationary phase (long overnight). 3- FX288: EGV140 (oriL3) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 4- FX289:EGV140 (oriL3) grown in M9 minimal medium supplemented with 0.4 % fructose to stationary phase (long overnight). 5- FX290: EGV111 (oriR4) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 6- FX291:EGV111 (oriR4) grown in M9 minimal medium supplemented with 0.4 % fructose to stationary phase (long overnight). 7- FX355:EPV50 (WT) grown in LB medium to exponential phase (0.2 OD 650nm) 8- FX356:EPV50 (WT) grown in LB medium to stationary phase (overnight) 9- FX286:EGV140 (oriL3) grown in LB medium to exponential phase (0.2 OD 650nm) 10- FX287:EGV140 (oriL3) grown in LB medium to stationary phase (overnight) 11- FX292:EGV111 (oriR4) grown in LB medium to exponential phase (0.2 OD 650nm) 12- FX49: MCH1 (WT monochromosome) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 13- FX48: MCH1 (WT monochromosome) grown in M9 minimal medium supplemented with 0.4 % fructose to stationary phase (long overnight). 14- FX11: EGV369 (oriL3 monochromosome) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 15- FX12: EGV366 (oriR4 monochromosome) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 16- FX296 EPV50 M9 Exp 17- FX294 EPV50 M9 Stat 18-FX316 EGV140 M9 Exp 19- FX315 EGV111 M9 Exp 20-FX318 MCH1 M9 Exp 21- FX317 MCH1 M9 Stat 22- FX320 EGV369 M9 Exp 23- FX319 EGV366 M9 Exp Chromosomal DNA was extracted using the Sigma GenElute bacterial genomic DNA kit. 5 μg of DNA were used to generate a genomic library according to Illumina's protocol. The libraries and the sequencing were performed by the High-throughput Sequencing facility of the I2BC (http://www.i2bc.paris-saclay.fr/spip.php?article399〈=en,CNRS, Gif-sur-Yvette, France). Genomic DNA libraries were made with the ‘Nextera DNA library preparation kit’ (Illumina) following the manufacturer’s recommendations. Library quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit (Agilent technologies). Libraries were pooled in equimolar proportions. 75 bp single reads were generated on an Illumina MiSeq instrument, using a MiSeq Reagent kit V2 (500 cycles) (Illumina), with an expected depth of 217X. Reads were aligned on the in silico reconstituted genome of the cognate strain using BWA software. An in-lab written MATLAB-based script was used to perform marker frequency analysis. Data were normalized by dividing uniquely mapping sequence reads by the total number of reads. Enrichment of uniquely mapping sequence reads in 1 kb non-overlapping windows were calculated and plotted against the chromosomal coordinates.
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