GEO DataSets

(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) RNA modifications have a substantial impact on tRNA function. While modifications in the anticodon loop play an important role in translational fidelity, modifications in the tRNA core influence tRNA structural stability. In bacteria, tRNA modifications play important roles in the stress response and expression of virulence factors. While tRNA modifications are well characterized in a few model organisms, our knowledge of tRNA modifications in human pathogens, such as Pseudomonas aeruginosa is lacking. more...

Organism:

Pseudomonas aeruginosa PA14; Escherichia coli BW25113

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL33546 GPL25344 GPL30881

27 Samples

Download data: CSV, FA, TXT

(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) 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 K-12

Type:

Other

Platform:

GPL30519

4 Samples

Download data: BEDGRAPH

(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

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

Organism:

Escherichia coli str. K-12 substr. MG1655; Staphylococcus aureus; Pseudomonas aeruginosa PAO1

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL28916 GPL27158 GPL26592

21 Samples

Download data: NARROWPEAK, TXT, XLSX

(Submitter supplied) Biofilms are heterogeneous bacterial communities featured by high persister prevalence, responsible for antibiotic tolerance. However, the mechanisms underlying persister formation within biofilms remained ambiguous. Here, by developing and utilizing a ribosomal RNA depleted bacterial single-cell RNA-seq method, RiboD-mSPLiT, we resolved biofilm heterogeneity and discovered pdeI as a marker gene for persister subgroup within biofilms. more...

Organism:

Escherichia coli str. K-12 substr. MG1655; Pseudomonas aeruginosa PAO1; Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26592 GPL28916 GPL27158

14 Samples

Download data: TXT, XLSX

(Submitter supplied) Biofilms are heterogeneous bacterial communities featured by high persister prevalence, responsible for antibiotic tolerance. However, the mechanisms underlying persister formation within biofilms remained ambiguous. Here, by developing and utilizing a ribosomal RNA depleted bacterial single-cell RNA-seq method, RiboD-mSPLiT, we resolved biofilm heterogeneity and discovered pdeI as a marker gene for persister subgroup within biofilms. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26592

1 Sample

Download data: TXT, XLSX

(Submitter supplied) Biofilms are heterogeneous bacterial communities featured by high persister prevalence, responsible for antibiotic tolerance. However, the mechanisms underlying persister formation within biofilms remained ambiguous. Here, by developing and utilizing a ribosomal RNA depleted bacterial single-cell RNA-seq method, RiboD-mSPLiT, we resolved biofilm heterogeneity and discovered pdeI as a marker gene for persister subgroup within biofilms. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26592

6 Samples

Download data: NARROWPEAK

(Submitter supplied) Our focus of this study is to determine the differential expression of genes related to uptake and degradation of nitrogenous compounds in E. coli colonizing the mouse intestine as compared to E. coli grown in minimal medium in vitro. We colonized CD-1 male mice with E. coli MG1655 StrR wild type and extracted the total RNA from mouse cecal mucus (GSE217743). We also colonized CD-1 male mice with E. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26592

10 Samples

Download data: WIG

(Submitter supplied) The antibiotic fosfomycin is widely recognized for treatment of lower urinary tract infections caused by Escherichia coli and lately gained importance as a therapeutic option to combat multidrug resistant bacteria. Still, resistance to fosfomycin frequently develops through mutations reducing its uptake. Whereas the inner membrane transport of fosfomycin has been extensively studied in E. coli, its outer membrane (OM) transport remains insufficiently understood. more...

Organism:

Escherichia coli BW25113

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26343

3 Samples

Download data: TXT

(Submitter supplied) While DNA N6-methyl-deoxyadenosine (6mA) is abundant in bacteria and protists, its presence and function in mammalian genomes have been less clear. We present Direct-Read 6mA sequencing (DR-6mA-seq), an antibody-independent method to measure 6mA at base-resolution with high sensitivity. DR-6mA-seq employs a unique mutation-based strategy to reveal 6mA sites as misincorporation signatures without any chemical or enzymatic modulation of 6mA. more...

Organism:

synthetic construct; Escherichia coli; Mus musculus; Escherichia coli K-12

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

67 Samples

Download data: NARROWPEAK, TXT

(Submitter supplied) RpoD is a houskeeping sigma factor and RpoN is an alternative one. It was identified their intragenic and intergenic binding sites and association with the RNA polymerase.

Organism:

Escherichia coli str. K-12 substr. MG1655; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17439 GPL22503

8 Samples

Download data: GFF

(Submitter supplied) Antisense RNAs (cis-asRNAs) in prokaryotes are more pervasive than originally thought. However, little is known about their expression patterns and functions. Here we determined transcriptomes and proteomes of E. coli at multiple time points in five culture conditions using directional RNA-seq and tandem mass spectrometry.

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL19529 GPL19530

22 Samples

Download data: CSV

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

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL17439 GPL22503

10 Samples

Download data: GFF

(Submitter supplied) Bacterial small regulatory RNAs (sRNAs) regulate gene expression by base-pairing to their target mRNAs. In Escherichia coli and many other bacteria, this process is dependent on the RNA chaperone Hfq, which binds sRNAs and mRNAs on different faces. YhbS (renamed here as HqbA), a putative Gcn5-related N-acetyltransferase (GNAT), was identified as a novel silencer of sRNA signaling in a genomic library screen. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18956

24 Samples

Download data: XLSX