GEO DataSets

(Submitter supplied) C-di-GMP signaling can directly influence bacterial behavior by affecting the functionality of c-di-GMP-binding proteins. In addition, c-di-GMP can exert an indirect and more global effect on gene transcription or translation, e.g. via riboswitches or by binding to transcription factors. In this study, we investigated the effects of changes in intracellular c-di-GMP levels on gene expression and protein production in the opportunistic pathogen Pseudomonas aeruginosa. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28916 GPL18782

20 Samples

Download data: CSV, TXT

(Submitter supplied) Most habitats on earth are colonized by diverse bacterial communities, offering ample opportunities for inter-species interactions. While competition for space and nutrients might often dominate such interactions, little is known about whether bacteria can sense competitors and mount specific responses to withstand their attacks. The competition-sensing hypothesis proposes that bacteria can do so through nutrient stress and cell damage cues. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18782

18 Samples

Download data: TXT

(Submitter supplied) Here, we used a saturated transposon insertion mutant pool of P. aeruginosa strain PAO1 and transposon insertion sequencing (Tn-Seq), to identify genes conditionally important for survival under conditions mimicking the environment of a nosocomial infection. Conditions tested included tissue culture medium with and without human serum, a murine abscess model, and a human skin organoid model.

Organism:

Pseudomonas aeruginosa PAO1

Type:

Other

Platform:

GPL18782

27 Samples

Download data: CSV, WIG

(Submitter supplied) Purpose: We wanted to determine the transcriptome profile of PAO1 wild type, PAO1ΔrhlE1, PAO1ΔrhlE2 and PAO1ΔrhlE1ΔrhlE2 mutants on swarming conditions. Method: Cells were harvested using the RNA bacteria protect solution (QIAGEN). Total RNAs was extracted and purified using Monarch RNA isolation kit (NEB), treated with DNase I (Promega) three times to remove contaminating genomic DNA and re-purified again using phenol-chloroform. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18782

8 Samples

Download data: FASTA, TXT

(Submitter supplied) It has been shown that the filamentous phage, Pf4, plays an important role in biofilm development, stress tolerance, genetic variant formation and virulence in Pseudomonas aeruginosa PAO1. These behaviours are linked to the appearance of superinfective phage variants. Here, we have investigated the molecular mechanism of superinfection as well as how the Pf4 phage can control host gene expression to modulate host behaviours. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

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

Platforms:

GPL18782 GPL20786

11 Samples

Download data: BEDGRAPH, CSV, NARROWPEAK, TXT

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

Organism:

Pseudomonas aeruginosa PAO1

Type:

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

Platforms:

GPL23999 GPL15987 GPL18782

27 Samples

Download data: BW, WIG

(Submitter supplied) In the opportunistic pathogen Pseudomonas aeruginosa the alp system encodes a programmed cell death (PCD) pathway that is switched on in a subset of cells in response to DNA damage. Here we show that the central regulator of this pathway, AlpA, exerts its effects by acting as an antiterminator rather than a transcription activator. In particular, we present evidence that AlpA positively regulates the alpBCDE cell lysis genes, as well as genes in a second newly identified operon, by recognizing specific DNA sites within the promoter, then binding RNA polymerase directly and allowing it to bypass intrinsic terminators positioned downstream. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18782

12 Samples

Download data: BW

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

Organism:

Pseudomonas aeruginosa PAO1

Type:

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

Platforms:

GPL28916 GPL18782

36 Samples

Download data

(Submitter supplied) The H-NS-like proteins MvaT and MvaU act coordinately as global repressors in Pseudomonas aeruginosa by binding to AT-rich regions of the chromosome. Although cells can tolerate the loss of either protein, identifying their combined regulatory effects has been challenging because the loss of both proteins is lethal due to induction of prophage Pf4 and subsequent superinfection of the cell. In other bacteria, H-NS promotes cellular fitness by inhibiting intragenic transcription from AT-rich target regions, preventing them from sequestering RNA polymerase; however, it is not known if whether MvaT and MvaU function similarly. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18782

21 Samples

Download data: BED, WIG

(Submitter supplied) Pseudomonas aeruginosa causes severe multi-drug resistant infections that often lead to bacteremia and sepsis. Physiologically relevant conditions can increase the susceptibility of pathogens to antibiotics, such as azithromycin (AZM). When compared to minimal inhibitory concentrations (MIC) in lab media, AZM had a 16-fold lower MIC in tissue culture medium with 5% MHB, and a 64-fold lower MIC in this tissue culture medium with 20% human serum. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18782

18 Samples

Download data: TXT

(Submitter supplied) Purpose: Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that undergoes swarming motility in response to semisolid conditions with amino acids as a nitrogen source. With a genome encoding hundreds of potential intergenic small RNAs (sRNAs), P. aeruginosa can easily adapt to different conditions and stresses. We previously identified 20 sRNAs dysregulated under swarming conditions and here provide phenotypic characterization for these sRNAs. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18782

10 Samples

Download data: TXT

(Submitter supplied) The goals of this study are to use Next-generation sequencing (NGS)to detect bacterial mRNA profiles of Pseudomonas aeruginosa PAO1 in response to 0, 1, 20 and 25 mg/L AgNPs or 0, 1,30 and 300 mg/L AgNRs for 2 h, using Illumina HiSeq 2500.The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18782

8 Samples

Download data: XLSX

(Submitter supplied) The stringent stress response, mediated by the signalling molecule guanosine penta(tetra)-phosphate (p)ppGpp, has recently gained more attraction as a potential new therapeutic target. However, interference of a global mediator could lead to unwanted side effects, therefore warrants detailed mechanistic understanding. We used RNA-Seq to investigate the transcriptional landscape of a Pseudomonas aeruginosa ppGpp-deficient strain under non-stressful conditions. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18782

6 Samples

Download data: TXT

(Submitter supplied) Pseudomonas virus PA5oct has a large, linear, double-stranded DNA genome (286,783 bp) and is related to Escherichia phages 121Q/PBECO 4, Klebsiella phage vB_KleM-RaK2, Klebsiella phage K64-1, and Cronobacter phage vB_CsaM_GAP32. A protein-sharing network analysis highlights the conserved core genes within this clade. Combining hybrid genome sequencing, RNA-Seq and mass spectrometry analyses of its virion proteins allowed us to accurately identify genes and elucidate regulatory elements for this phage (ncRNAs, tRNAs and promoter elements). more...

Organism:

Pseudomonas aeruginosa PAO1; Pseudomonas virus PA5oct

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26557 GPL18782

13 Samples

Download data: FNA, GFF3, XLSX

(Submitter supplied) Purpose: Pseudomonas aeruginosa is a motile species that initiates swarming motility in response to specific environmental cues, i.e., a semisolid surface with amino acids as a nitrogen source (relevant to the human lung). Swarming is an intricately regulated process, but to date post-transcriptional regulation has not been extensively investigated. Small non-coding RNAs (sRNA) are hypothesized to play post-transcriptional regulatory roles, largely through suppression of translation, and we previously demonstrated 20 sRNA species that were dysregulated under swarming conditions. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18782

10 Samples

Download data: TXT

(Submitter supplied) Transcriptional response of P. aeruginosa grown in the presence of 2.5 micromolar testosterone.

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18782

4 Samples

Download data: CSV

(Submitter supplied) ClpV3 is a cytoplasmic AAA+ ATPase protein and is an essential component of H3-T6SS in Pseudomonas aeruginosa. Here, we report that an H3-T6SS deletion mutant PAO1(ΔclpV3) significantly affected the virulence-related phenotypes including pyocyanin production, biofilm formation, proteolytic activity and motilities. Most interestingly, the expression of T3SS genes was markedly affected, indicating a strong link between H3-T6SS and T3SS. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18782

4 Samples

Download data: XLSX

(Submitter supplied) In the opportunistic pathogen Pseudomonas aeruginosa RsmA is an RNA-binding protein that plays critical roles in the control of virulence, interbacterial interactions and biofilm formation. Although RsmA is thought to exert its regulatory effects by binding full-length transcripts, the extent to which RsmA binds nascent transcripts has not been addressed. Moreover, which transcripts are direct targets of this key post-transcriptional regulator is largely unknown. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

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

Platforms:

GPL23999 GPL18782

30 Samples

Download data: BED, BW, TXT, WIG

(Submitter supplied) Antibiotic-resistant “super-bug” bacteria represent a global health problem with no imminent solutions. Here, we demonstrate that AB569 (acidified nitrite (A-NO2-) and Na2-EDTA) killed all Gram-negative and Gram-positive bacteria tested. AB569 was also efficacious at killing the model organism P. aeruginosa in biofilms and in a murine chronic lung infection model. AB569 was not toxic to human cell lines at bactericidal concentrations. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18782

11 Samples

Download data: TXT

(Submitter supplied) Hfq is an RNA chaperone and an important post-transcriptional regulator in bacteria. Using chromatin immunoprecipitation together with DNA sequencing (ChIP-Seq), we show that Hfq associates with hundreds of different regions of the Pseudomonas aeruginosa chromosome. These associations are abolished when transcription is inhibited, indicating they reflect Hfq binding to transcripts during their synthesis. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18782

20 Samples

Download data: BED, WIG