Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA102773 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description: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)
| PRJNA697923 | ENA
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.
2024-05-21 | PXD041209 | Pride
Project description:The physiological role of the various nucleoid-associated proteins in bacteria and HU in particular has been addressed in a number of studies but remains so far not fully understood. In this work, a genome-wide microarray hybridization approach, combined with in vivo genetic experimentation, has been performed in order to compare and evaluate the effect of HUalpha, HUbeta and HUalphabeta on the transcription of the Escherichia coli K12 genes as a function of growth phase. The histone-like protein HU is present in the E. coli cell under three dimeric forms (HUalphabeta, HUalpha2 and HUbeta2) in a ratio that varies with growth phase. The experimental protocol is designed to handle strain genotype and growth phase as independent variables. Experiment Overall Design: We used microarrays to investigate global bacterial gene expression in five genotypes of E. coli C600: WT (JO2057), hupA (JO2081), hupB (JO2083), hupAB (JO3020) and rpoS (MW30) at three growth growth phases: exponential, transition and stationary and in three growth media: LB, M9 minimal Glucose and M9 minimal Glycerol. The most relevant experiments were carried out in duplicate: the wild type (JO2057) and the hupAB (JO3020) strains were tested in the exponential and stationary phase, in LB. Wild type and hupAB strains were also tested in single experiments at the transition phase in LB. The single hupA (JO2081) and single hupB (JO2083) mutants were tested at the three growth phases in LB. Wild type and hupAB strains were compared in single experiments both in M9 Minimal Glucose and M9 Minimal Glycerol at the exponential and stationary phase. The last chips were used to test respectively the rpoS mutant at the at the exponential and stationary phase in LB.
2009-01-14 | E-GEOD-11183 | biostudies-arrayexpress
Project description:E. coli CFT073 gene expression at t= 4 hours after a temperature upshift from 23˚C to 37˚C (M9 minimal glycerol medium, exponential phase growth)
| PRJNA779445 | ENA
Project description:Growth to mid exponential phase in M9 minimal media supplemented with 0.5% maltose 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% maltose Keywords: Logical Set
2006-05-20 | GSE4876 | GEO
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
2006-05-20 | GSE4875 | GEO
Project description:The gene expression profile of MC4100 delta rsd with pACYC Rsd and pACYC delta BS plasmids has been analysed using whole genome oligonucleotide microarrays. Control RNA was isolated from 50ml LB cultures of MC4100 delta rsd strain with pACYC delta BS. Experimental RNA was isolated from 50ml LB cultures of MC4100 delta rsd with pACYC Rsd, for each growth condition (OD600 = 0.4: log phase, 0.9: late log phase, 1.1: transition phase, ST(OD600 = >2.0): stationary phase). The experiments performed replicate. Keywords: timecourse (overproduction of Rsd)
2007-10-22 | GSE5981 | 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.
2021-05-07 | E-MTAB-7193 | biostudies-arrayexpress
Project description:The goal of this analysis was to perform transcriptome-wide quantification of genes expressed in E.coli BW25113 when it is grown in M9 with 2.2 g/L glycerol, M9 + 3.3 g/L sodium pyruvate, or M9 + 2.2 g/L glycerol + 2 g/L casamino acids. With this data, we aimed to determine the fractional abundance of certain transcripts, and relate that to the fractional abundance of the proteins they code for (see proteomics data in Schmidt et al 2016).
2025-12-31 | E-MTAB-15217 | biostudies-arrayexpress
Project description:We propose an optimized protocol to reconstruct bacterial transcriptional regulatory networks (TRNs) using ChIP-exo and RNA-seq datasets. For the reconstruction of TRNs, the omics datasets were targeted to RpoS and generated in Escherichia coli K-12 MG1655 cultured at mid-exponential phase in M9 glucose media.
2026-06-20 | GSE271232 | GEO