Genome-wide RNA-sequencing of E. coli strain 55989 from in vitro and in vivo samples
Ontology highlight
ABSTRACT:
ORGANISM(S): Escherichia coli 55989
PROVIDER: GSE165634 | GEO | 2021/01/28
REPOSITORIES: GEO
Similar Datasets
Project description:We performed Hi-C analysis of Escherichia coli MG1655 cells in exponential and stationary growth phase. We could detect long-range interactions predominantly in the Ori domain of the chromosome. Interestingly, the use of a new type of control revealed that these interactions are mostly crosslinking independent.
2015-09-01 | GSE61658 | GEO
Project description:We performed Hi-C analysis of Escherichia coli MG1655 cells in exponential and stationary growth phase. We could detect long-range interactions predominantly in the Ori domain of the chromosome. Interestingly, the use of a new type of control revealed that these interactions are mostly crosslinking independent. 6 samples from exponential phase growth in M9 medium; 6 samples from stationary phase growth in M9 medium; for each growth condition, 3 samples were with crosslinking and 3 samples were without.
2015-09-01 | E-GEOD-61658 | biostudies-arrayexpress
Project description:The role of rpoS gene in the formation of Escherichia coli biofilms were investigated. The gene expression was compared among E. coli MG1655 wild type strain and rpoS knock-out strain in the biofilms, the planktonic exponential phase, and the planktonic stationary phase. The analysis revealed that the wild type bilfilms (WBF) showed similar pattern of gene expression with the WT planktonic stationary phase (WS), whereas the rpoS knock-out biofilms (MBF) showed similar pattern of gene expression with the wild type planktonic exponential phase (WE). Genes involved in the energy metabolism and the flagella synthesis showed higher expression in the rpoS knock-out biofilms (MBF), but not in the wild type biofilms (WBF). Moreover, genes involved in the stress responses showed higher expression in the wild type biofilms (WBF), but not in the rpoS knock-out biofilms (MBF). Keywords: cell type comparison (biofilms vs planktonic cells, wild type vs rpoS knock-out strains)
2008-05-23 | GSE7885 | GEO
Project description:We have deep sequenced the small transcriptome of Escherichia coli growing in LB and in MOPS, in exponential and stationary phase, and analyzed the resulting reads by a novel pipeline STARPA (Stable RNA Processing Product Analyzer). Our analysis reveals over 14,000 small transcripts enriched during both growth stages. RNA samples were collected from total RNA pools or from crude ribosome pools and then size selected by electrophoresis to limit the products to 20-300nt.
2020-11-21 | GSE161907 | GEO
Project description:Background: Global patterns of gene expression of Escherichia coli K-12 during growth transitions have been deeply investigated, however, comparable studies of E. coli O157:H7 have not been explored, particularly with respect to factors regulating virulence genes and genomic islands specific to this pathogen. To examine the impact of growth phase on the dynamics of the transcriptome, O157:H7 Sakai strain was cultured in MOPS minimal media (0.1% glucose), RNA harvested at 10 time points from early exponential to full stationary phase, and relative gene expression was measured by co-hybridization on high-density DNA microarrays. Results: Analysis of variance (R/MAANOVA, Fs test) identified 442 (36%) of 1239 O157-specific ORFs and 2110 (59%) of 3647 backbone ORFs that changed in expression significantly over time. QT cluster analysis placed 2468 of the 2552 significant ORFs into 12 groups; each group representing a distinct expression pattern. ORFs from the largest cluster (n=1078) decreased in expression from late exponential to early stationary phase: most of these ORFs are involved in functions associated with steady state growth. Also represented in this cluster are ORFs of the TAI island, encoding tellurite resistance and urease activity, which decreased ~4-fold and most ORFs of the LEE island, which decreased ~2-fold by early stationary phase. ORFs encoding proteins secreted via the LEE encoded type III secretion system, such as tccP and espJ, also decreased in expression from exponential to stationary phase. Three of the clusters (n=154) comprised genes that are transiently upregulated at the transition into stationary phase and included genes involved in nutrient scavenging. Upregulated genes with an increase in mRNA levels from late exponential to early stationary phase belonged to one cluster (n=923) which includes genes involved in stress responses (e.g. gadAB, osmBC, and dps). These transcript levels remained relatively high for >3h in stationary phase. The Shiga toxin genes (stx1AB and stx2B) were significantly induced after transition into stationary phase. Conclusions: Expression of 307 O157-specific ORFs was modulated in a growth dependent manner. These results provide a baseline transcriptional profile that can be compared to patterns of gene expression of this important foodborne pathogen under adverse environmental conditions. Keywords: time course
2007-06-15 | GSE7477 | GEO
Project description:The transition between exponential and stationary phase is a natural phenomenon for all bacteria and requires a massive readjustment of the bacterial transcriptome. Exoribonucleases are key enzymes in the transition between the two growth phases. PNPase, RNase R and RNase II are the major degradative exoribonucleases in Escherichia coli. We analysed the whole transcriptome of exponential and stationary phases from the WT and mutants lacking these exoribonucleases (Δpnp, Δrnr, Δrnb, and ΔrnbΔrnr). When comparing the cells from exponential phase with the cells from stationary phase more than 1000 transcripts were differentially expressed, but only 491 core transcripts were common to all strains. There were some differences in the number and transcripts affected depending on the strain, suggesting that exoribonucleases influence the transition between these two growth phases differently. Interestingly, we found that the double mutant RNase II/RNase R is similar to the RNase R single mutant in exponential phase while in stationary phase it seems to be closer to the RNase II single mutant. This is the first global transcriptomic work comparing the roles of exoribonucleases in the transition between exponential and stationary phase.
2019-11-13 | GSE117635 | GEO
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:Proteomic data from E. coli grown with or without the azo dye, Red Dye number 40. WT and delta fnr E. coli were cultured in Luria Broth media and cultures were inoculated with 250 uM Red No. 40 at either mid-exponential or stationary growth phases. Vehicle control samples were also analyzed at mid-exponential and stationary growth phases.
2023-07-06 | MSV000092365 | MassIVE
Project description:Analysis of the contribution of the post-transcriptional regulator CsrA to translation during exponential growth in Escherichia coli
2019-02-05 | GSE107834 | GEO
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