GEO DataSets

(Submitter supplied) Purpose: The purpose of this study was to investigate the effect of quorum sensing on phage infection. Methods: We constructed the lasR gene knockout strain of Pseudomonas aeruginosa PAO1 and performed transcriptome sequencing.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18644

6 Samples

Download data: TSV, TXT

(Submitter supplied) Methylrhodomelol (1) is a bromophenol from the red alga Vertebrata lanosa (L.) T.A.Christensen that has been associated with antimicrobial properties. Aim of the current study was therefore, to assess the antimicrobial potential of this compound in more detail against the gram-negative pathogen Pseudomonas aeruginosa. 1 exerted weak bacteriostatic activity against different strains when grown in minimal medium, whereas other phenolics were inactive. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33271

6 Samples

Download data: TXT

(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:

Escherichia coli BW25113; Pseudomonas aeruginosa PA14

Type:

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

Platforms:

GPL25344 GPL30881 GPL33546

27 Samples

Download data: CSV, FA, TXT

(Submitter supplied) Efflux pumps of the resistance-nodulation-division (RND) superfamily, particularly the AcrAB-TolC and MexAB-OprM, besides mediating intrinsic and acquired resistance, also intervene in bacterial pathogenicity. Inhibitors of such pumps could restore activities of antibiotics and curb bacterial virulence. Here, we identify pyrrole-based compounds that boost antibiotic activity in Escherichia coli and Pseudomonas aeruginosa by inhibiting their archetype RND transporters. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26913

6 Samples

Download data: XLSX

(Submitter supplied) The opportunistic pathogen Pseudomonas aeruginosa has complex quorum sensing (QS) circuitry, which involves two acylhomoserine lactone (AHL) systems, the LasI AHL synthase and LasR AHL-dependent transcriptional activator system and the RhlI AHL synthase-RhlR AHL-responsive transcriptional activator. There is also a quinoline signaling system (the Pseudomonas quinolone signal, PQS, system). Although there is a core set of genes regulated by the AHL circuits, there is substantial strain-to-strain variation in the non-core QS regulated genes. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24583

16 Samples

Download data: CSV, TXT

(Submitter supplied) The surge of antimicrobial resistance in recent decades threatens efficacy of current antibiotics, particularly against Pseudomonas aeruginosa, a highly resistant gram-negative pathogen. The asymmetric outer membrane of P. aeruginosa combined with its array of efflux pumps provide a barrier to xenobiotic intracellular accumulation, thus making the discovery of novel drugs with whole cell antibacterial activity very challenging. more...

Organism:

Pseudomonas aeruginosa UCBPP-PA14

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27892

30 Samples

Download data: CSV

(Submitter supplied) The surge of antimicrobial resistance in recent decades threatens efficacy of current antibiotics, particularly against Pseudomonas aeruginosa, a highly resistant gram-negative pathogen. The asymmetric outer membrane of P. aeruginosa combined with its array of efflux pumps provide a barrier to xenobiotic intracellular accumulation, thus making the discovery of novel drugs with whole cell antibacterial activity very challenging. more...

Organism:

Pseudomonas aeruginosa UCBPP-PA14

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27892

60 Samples

Download data: CSV

(Submitter supplied) The global transcriptional profiles of Pseudomonas aeruginosa phages LUZ19, LUZ24, YuA, PAK_P3, 14-1 and phiKZ was obtained using the long read RNA sequencing technique ONT-cappable-seq. Using this approach we obtained a comprehensive genome-wide map of viral transcription start sites, terminators and transcription units.

Organism:

Pseudomonas aeruginosa

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL31946

12 Samples

Download data: NARROWPEAK

(Submitter supplied) Large-genome bacteriophages (jumbo phages) of the Chimalliviriadae family assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and CRISPR/Cas nucleases. While the nuclear shell provides broad protection against host nucleases, it necessitates transport of mRNA out of the nucleus-like compartment for translation by host ribosomes, and transport of specific proteins into the nucleus-like compartment to support DNA replication and mRNA transcription. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24583

8 Samples

Download data: BED, BW

(Submitter supplied) The ΔcrcZ mutant shows constitutive repression of all crc/Hfq target genes in the translation. Therefore, it presents a hyper‐repressed phenotype (more repressed than the parental strain) in the acquisition of secondary carbon sources, even though the preferred carbon source is not present. Δcrc is more sensitive to antibiotics, more susceptible to oxidative stress, and less motile than the parental strain. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15987

11 Samples

Download data: TXT

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

Organism:

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

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; Staphylococcus aureus; Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28916 GPL27158 GPL26592

14 Samples

Download data: TXT, XLSX

(Submitter supplied) The overall success of bacterial pathogens depends on the coordinated expression of virulence determinants. Regulatory circuits that drive pathogenesis are complex, multilayered and incompletely understood. Here, we reveal that alterations in tRNA modifications define pathogenic phenotypes in the opportunistic pathogen Pseudomonas aeruginosa. We demonstrate that the enzymatic activity of GidA leads to the introduction of a carboxymethylaminomethyl modification in selected tRNAs. more...

Organism:

Pseudomonas aeruginosa UCBPP-PA14

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL27892

12 Samples

Download data: BED

(Submitter supplied) The overall success of a pathogenic microbe depends on the coordinated expression of virulence determinants. Regulatory circuits that drive pathogenesis are complex, multilayered and often not completely understood. Here, we reveal that alterations in tRNA modifications define pathogenic phenotypes in the opportunistic pathogen Pseudomonas aeruginosa. Growth phase-dependent enzymatic activity of GidA leads to differential introduction of carboxymethylaminomethyl-uridine (cmnm5U34) at uridine 34 of the anticodon of selected tRNAs. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18287

6 Samples

Download data: XLSX

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

Organism:

Pseudomonas aeruginosa UCBPP-PA14; Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL18287 GPL27892

18 Samples

Download data: BED

(Submitter supplied) Pseudomonas aeruginosa and Staphylococcus aureus are often co-isolated in persistent infections. The goal of this study was to determine how secreted products from S. aureus affect gene expression in surface-associated P. aerguinosa undergoing emergent motility. Therefore, media salts control or S. aureus supernatant was added to agar plates at 25% total volume. P. aeruginosa was inoculated on the agar and gene expression was measured from the leading edge after 17 h incubation using RNA-seq. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21297

8 Samples

Download data: TXT

(Submitter supplied) Pseudomonas aeruginosa is a leading cause of hospital acquired infections for which the development of new antibiotics is urgently needed. Unlike most enteric bacteria, P. aeruginosa lacks thymidine kinase and thymidine phosphorylase activity, and thus cannot scavenge exogenous thymine. An appealing strategy to selectively target P. aeruginosa while leaving the healthy microbiome largely intact would thus be to disrupt thymidine synthesis while providing exogenous thymine. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33271

3 Samples

Download data: XLSX

(Submitter supplied) Discovering new bacterial signaling pathways offers unique antibiotic strategies. Here, through an unbiased resistance screen of 3,884 gene knockout strains, we uncovered a previously unknown non-lytic bactericidal mechanism that sequentially couples three transporters and downstream transcription to lethally suppress respiration of the highly virulent P. aeruginosa strain PA14 - one of three species on the WHO's 'Priority 1: Critical' list. more...

Organism:

Pseudomonas aeruginosa PA14

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31013

12 Samples

Download data: CSV

(Submitter supplied) The 280-kB giant bacteriophage PHIKZ expresses hundreds of transcripts upon infection of Pseudomonas aeruginosa. To illuminate which transcripts are the very first and abundant ones, we extracted RNA after infection and sequenced the transcripts. The early expressed genes promise to be important for surpassing the host defence systems and to reprogram the host machinery towards phage replication. We discovered a number of transcripts that encode for proteins which we found in an independent study to be associated with large complexes. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23999

12 Samples

Download data: WIG

(Submitter supplied) Azithromycin binds to the nascent peptide exit tunnel (NPET) close to the peptidyltransferase center (PTC) of the ribosome, which obstructs the NPET and subsequently induces ribosome stalling and depletion of intracellular pools of tRNAs. To understand the mechanism through which azithromycin represses the transcription of mutation promoting genes, we utilized ribosome profiling to analyze azithromycin caused redistribution of ribosomes on the cellular mRNAs. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL26913

4 Samples

Download data: XLSX