GEO DataSets

(Submitter supplied) Disinfectants are essential tools for controlling infectious diseases and maintaining sterile conditions in many medical and food-industry settings. Recent work revealed that a deficiency in the PTS carbohydrate phosphor transfer system confers pan-tolerance to killing by diverse disinfectant types through its interaction with the cAMP-CRP regulatory network. The present work characterized a new pan-tolerance mutant obtained by enrichment using phenol as a lethal probe and an Escherichia coli PTS null mutant as a parental strain. more...

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26856

4 Samples

Download data: TXT

(Submitter supplied) The rate and direction of phenotypic evolution depends on the availability of phenotypic variants induced either genetically or environmentally for selection act upon. Theoretical suggest that genetic interactions between genes governing phenotypes could explain how the bias in phenotypic variability arises. However, it remains unknown whether the phenotypic variability is explained by real known genetic interactions as expected. more...

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli

Type:

Expression profiling by array

Platform:

GPL18948

16 Samples

Download data: TXT

(Submitter supplied) Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based, transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hindered by the massive density of bacterial mRNA. To overcome this challenge, we combine 1000-fold volumetric expansion with multiplexed error robust fluorescence in situ hybridization (MERFISH) to create bacterial-MERFISH, a method enabling high-throughput, spatially resolved profiling of thousands of operons within individual bacteria. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21117 GPL26592

3 Samples

Download data: FASTA, SF

(Submitter supplied) Whether the emergence of a nascent protein from the ribosome and the formation of structural elements are synchronized has been a longstanding question. Paradoxically, kinetically efficient translation can induce mis-folding and aggregation despite the presence of molecular chaperones, which in Escherichia coli are induced by unfolded protein via σ32. The molecular mechanisms mediating translation efficiency and protein folding efficiency remain poorly understood. more...

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL18956 GPL18133

30 Samples

Download data: TSV

(Submitter supplied) Although many clinically important antibiotics inhibit bacterial ribosomes, the mechanisms by which bacterial cells rescue ribosomes stalled by antibiotics remain poorly understood. Ribosome stalling leads to collisions that recruit ribosome quality control (RQC) factors that recycle the ribosome subunits and target nascent proteins for degradation. Surprisingly, loss of known RQC factors in E. coli does not lead to significant antibiotic sensitivity, even though antibiotics stall ribosomes and induce collisions, suggesting the existence of additional, uncharacterized RQC mechanisms. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL21117

6 Samples

Download data: WIG

(Submitter supplied) RNC-seq experiment of the simulated acetylation mutant S1K247Q of S1 protein

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26592

6 Samples

Download data: TXT

(Submitter supplied) RNA-seq experiment of the simulated acetylation mutant S1K247Q of S1 protein

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26592

6 Samples

Download data: TXT

(Submitter supplied) Defining the cellular factors that drive growth rate and proteome composition is essential for understanding and manipulating cellular systems. In bacteria, ribosome concentration is known to be a constraining factor of cell growth rate, while gene concentration is usually assumed not to be limiting. Here, using single-molecule tracking, quantitative single-cell microscopy, and modeling, we show that genome dilution in Escherichia coli cells arrested for DNA replication results in a decrease in the concentration of active RNA polymerases and ribosomes. more...

Organism:

Caulobacter vibrioides; Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34296

8 Samples

Download data: BIGWIG

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL21117

75 Samples

Download data: BED, BW

(Submitter supplied) Bacteria defend themselves from viral predation using diverse immune systems, many of which sense and target foreign nucleic acids. Defense-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this immune strategy by instead leveraging DNA synthesis, but the identities and functions of their DNA products remain largely unknown. Here we show that DRT2 systems execute an unprecedented immunity mechanism that involves de novo gene synthesis via rolling-circle reverse transcription of a non-coding RNA (ncRNA). more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21117

3 Samples

Download data: BED

(Submitter supplied) Bacteria defend themselves from viral predation using diverse immune systems, many of which sense and target foreign nucleic acids. Defense-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this immune strategy by instead leveraging DNA synthesis, but the identities and functions of their DNA products remain largely unknown. Here we show that DRT2 systems execute an unprecedented immunity mechanism that involves de novo gene synthesis via rolling-circle reverse transcription of a non-coding RNA (ncRNA). more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL21117

36 Samples

Download data: BW

(Submitter supplied) Bacteria defend themselves from viral predation using diverse immune systems, many of which sense and target foreign nucleic acids. Defense-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this immune strategy by instead leveraging DNA synthesis, but the identities and functions of their DNA products remain largely unknown. Here we show that DRT2 systems execute an unprecedented immunity mechanism that involves de novo gene synthesis via rolling-circle reverse transcription of a non-coding RNA (ncRNA). more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL21117

36 Samples

Download data: BW

(Submitter supplied) We examined the DNA damage response of bacterium E. coli using the replication inhibitor azidothyimdine (AZT), and RNA-Seq analysis. We confirm the induction of classic SOS loci by AZT and identify several genes, including many of the pyrimidine pathway, that are induced dependent on LexA cleavage, but have not been previously demonstrated to be DNA damage-inducible. Despite a strong dependence on LexA, these genes lack LexA boxes and their regulation by LexA is likely to be indirect via unknown factors. more...

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24020

16 Samples

Download data: TSV

(Submitter supplied) Bacteria often evolve antibiotic resistance through mutagenesis. However, the processes causing the mutagenesis have not been fully resolved. Here we found that a broad range of ribosome-targeting antibiotics caused mutations through an underexplored pathway. Focusing on the clinically important aminoglycoside gentamicin, we found that the translation inhibitor caused genome-wide premature stalling of RNA polymerase (RNAP) in a loci-dependent manner. more...

Organism:

Escherichia coli BW25113

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27123

24 Samples

Download data: CSV, XLSX

(Submitter supplied) Total RNA was extracted and sequenced from Escherichia coli cultured to log phase and stable phase at 37 ° C and 45 ° C, respectively. The transcriptome data of Escherichia coli under four different growth conditions were obtained.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24659

12 Samples

Download data: TXT

(Submitter supplied) Chromosome conformation capture and sequencing experiments were carried out at 37℃ and 45℃ for E. coli in logarithmic phase and stable phase, respectively. Three-dimensional DNA interaction data of E. coli under four different growth conditions and control group were obtained

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL24659

10 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24659

22 Samples

Download data: TXT

(Submitter supplied) Microbial physiology plays a pivotal role in construction of a superior microbial cell factory for efficient production of desired products. Here we identified pcnB repression through genome-scale CRISPRi modulation combining fluorescence-activated cell sorting (FACS) and next-generation sequencing (NGS), which confers improved physiology for free fatty acids (FFAs) overproduction in Escherichia coli. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL26592

5 Samples

Download data: XLSX

(Submitter supplied) Microbial physiology plays a pivotal role in construction of a superior microbial cell factory for efficient production of desired products. Here we identified pcnB repression through genome-scale CRISPRi modulation combining fluorescence-activated cell sorting (FACS) and next-generation sequencing (NGS), which confers improved physiology for free fatty acids (FFAs) overproduction in Escherichia coli. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34485

6 Samples

Download data: XLS

(Submitter supplied) Many neutralophilic bacterial species try to evade acid stress with an escape strategy, which is reflected in the increased expression of genes coding for flagellar components. Extremely acid-tolerant bacteria, such as Escherichia coli, survive the strong acid stress, e.g. in the stomach of vertebrates. Recently, we were able to show that the induction of motility genes in E. coli is strictly dependent on the degree of acid stress, i.e. more...

Organism:

Escherichia coli BW25113; Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32899 GPL34252

12 Samples

Download data: XLSX