GEO DataSets

(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) 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) 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

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

Organism:

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

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL30519 GPL33080

102 Samples

Download data: BEDGRAPH

(Submitter supplied) How biomolecules condense to organize subcellular processes is of fundamental significance. Nitrogen-starved Escherichia coli form a single condensate, which we termed Bacterial Stress Body (BSB). Its formation is triggered by long polyphosphate chains, which scaffold the RNA chaperone Hfq into high molecular weight complexes with distinct sequence-specific RNA and DNA binding properties. We show that polyP is crucial for the stabilization of select RNAs, the sequestration of translation- and RNA metabolism-associated proteins that likely stall protein synthesis, and the specific nucleoid-associated localization of BSBs. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL33080

42 Samples

Download data: CSV

(Submitter supplied) How biomolecules condense to organize subcellular processes is of fundamental significance. Nitrogen-starved Escherichia coli form a single condensate, which we termed Bacterial Stress Body (BSB). Its formation is triggered by long polyphosphate chains, which scaffold the RNA chaperone Hfq into high molecular weight complexes with distinct sequence-specific RNA and DNA binding properties. We show that polyP is crucial for the stabilization of select RNAs, the sequestration of translation- and RNA metabolism-associated proteins that likely stall protein synthesis, and the specific nucleoid-associated localization of BSBs. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33080

56 Samples

Download data: CSV

(Submitter supplied) We report using global regulator libraries based on the CRISPR-enabled trackable genome engineering (CREATE) method to engineer tolerance against multiple inhibitors in Escherichia coli. Deep mutagenesis libraries were rationally designed, constructed, and screened to target 34,340 mutations across 23 global regulators.These libraries were divided into G1, G2, G3, G4 and G5 sub-groups according to different gene functions (such as active sites, DNA binding sites, and predicted functional sites) . more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL21117

5 Samples

Download data: TXT

(Submitter supplied) In order to systematically assess the frequency and origin of stop codon recoding events, we designed a library of reporters. We introduced premature stop codons into mScarlet that enabled high-throughput quantification of protein synthesis termination errors in E. coli using fluorescent microscopy. We found that under stress conditions, stop codon recoding may occur with a rate as high as 80%, depending on the nucleotide context, suggesting that evolution frequently samples stop codon recoding events. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL33229

13 Samples

Download data: BAM

(Submitter supplied) The DNA damage inducible SOS response in bacteria serves to increase survival of the species. The SOS response first initiates error-free repair which is followed by error-prone repair. Here, we have employed a multi-omics approach to elucidate the temporal coordination of the SOS response using transcriptomics, signalomics, and metabolomics. Escherichia coli was grown in batch cultivation in bioreactors to ensure highly controlled conditions. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21117

42 Samples

Download data: CSV