GEO DataSets

(Submitter supplied) To determine the effects of phage m⏀11 on gene expression in USA300 (LAC*)

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27158

4 Samples

Download data: TXT

(Submitter supplied) To determine the effects of phage adenine methyltransferase (pamA) on gene expression in WT USA300 (LAC*)

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27158

5 Samples

Download data: TSV

(Submitter supplied) Small RNAs have been found to control a broad range of bacterial phenotypes including tolerance to antibiotics. Vancomycin tolerance in multidrug resistance Staphylococcus aureus is correlated with dysregulation of small RNAs although their contribution to antibiotic tolerance in poorly understood. RNA-RNA interactome profiling techniques are expanding our understanding of sRNA-mRNA interactions in bacteria; however, determining the function of these interactions for hundreds of sRNA-mRNA pairs is a major challenge. more...

Organism:

Staphylococcus aureus subsp. aureus str. JKD6008

Type:

Other

Platform:

GPL34143

10 Samples

Download data: TXT

(Submitter supplied) Small RNAs have been found to control a broad range of bacterial phenotypes including tolerance to antibiotics. Vancomycin tolerance in multidrug resistance Staphylococcus aureus is correlated with dysregulation of small RNAs although their contribution to antibiotic tolerance in poorly understood. RNA-RNA interactome profiling techniques are expanding our understanding of sRNA-mRNA interactions in bacteria; however, determining the function of these interactions for hundreds of sRNA-mRNA pairs is a major challenge. more...

Organism:

Staphylococcus aureus subsp. aureus str. JKD6008

Type:

Other

Platform:

GPL34143

2 Samples

Download data: TXT

(Submitter supplied) Small RNAs have been found to control a broad range of bacterial phenotypes including tolerance to antibiotics. Vancomycin tolerance in multidrug resistance Staphylococcus aureus is correlated with dysregulation of small RNAs although their contribution to antibiotic tolerance in poorly understood. RNA-RNA interactome profiling techniques are expanding our understanding of sRNA-mRNA interactions in bacteria; however, determining the function of these interactions for hundreds of sRNA-mRNA pairs is a major challenge. more...

Organism:

Staphylococcus aureus subsp. aureus str. JKD6008

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31256

6 Samples

Download data: TXT

(Submitter supplied) Staphylococcus aureus is an adaptable human pathogen causing life-threatening endocarditis and bacteraemia. Methicillin-resistant S. aureus (MRSA) is alarmingly common, and treatment is confined to last-line antibiotics. Vancomycin is the treatment of choice for MRSA bacteraemia and vancomycin treatment failure is often associated with vancomycin-intermediate S. aureus strains termed VISA. The regulatory 3’ UTR of vigR mRNA contributes to vancomycin tolerance in the clinical VISA isolate JKD6008 and upregulates the lytic transglycosylase IsaA. more...

Organism:

Staphylococcus aureus

Type:

Other

Platform:

GPL30817

4 Samples

Download data: BED, CSV, GFF

(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:

GPL27158 GPL28916 GPL26592

14 Samples

Download data: TXT, XLSX

(Submitter supplied) A total of 10 cDNA libraries were constructed, representing 3 and 2 independent biological replicates of S. aureus strain KES34 (unmodified ribosomes) and KES30 (m6A2058-modified ribosomes), respectively. Translational efficiency (RPF/mRNA ratios), total mRNA abundance and ribosome density of each ORFs were calculated.

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17452

10 Samples

Download data: TXT

(Submitter supplied) RNA samples were extracted from both the WT and isogenic mutant NMΔasp23, respectively, and then subjected to RNA-seq analysis.

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25144

6 Samples

Download data: TXT

(Submitter supplied) During the COVID-19 pandemic, facemasks have played a pivotal role in preventing person-person droplet transmission of viral particles. However, prolonged facemask wearing causes skin irritations colloquially referred to as ‘maskne’ (mask + acne), which manifests as acne and contact dermatitis and is mostly caused by pathogenic skin microbes. Previous studies revealed that the putative causal microbes were anaerobic bacteria, but the pathogenesis of facemask-associated skin conditions remains poorly defined. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25144

6 Samples

Download data: TXT

(Submitter supplied) Lipoproteins of the opportunistic pathogen Staphylococcus aureus play a crucial role in various cellular processes and host interactions. Consisting of a protein and a lipid moiety, they support nutrient acquisition and anchor the protein to the bacterial membrane. Recently, we identified several processed and secreted small linear peptides that derive from the secretion signal sequence of S. aureus lipoproteins. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27158

12 Samples

Download data: TXT

(Submitter supplied) Better understanding of S. aureus throat colonization in the presence of other competing/coexisting microbes may provide insight into S. aureus adaptation to the human throat and recurrence of infection. In this work, we explore the responses triggered by the encounter between two common throat bacteria, S. aureus and S. anginosus, in the presence of human tonsillar epithelial cells. We performed an in vitro coculture experiment followed by RNA sequencing. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28116

12 Samples

Download data: FASTA, TXT

(Submitter supplied) Safe and efficient antibacterial materials are urgently needed to combat drug-resistant bacteria and biofilm-associated infections. The rational design of nanoparticles for flexible elimination of biofilms by alternative strategies remains challenging. Herein, we propose the fabrication of Janus-structured nanoparticles targeting extracellular polymeric substance to achieve dispersion or near-infrared (NIR) light-activated photothermal elimination of drug-resistant biofilms, respectively. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29442

4 Samples

Download data: CSV

(Submitter supplied) We wished to examine the effect that coculture with Desemzia incerta would have on the S. aureus transcriptional profile. We have previously shown D. incerta to have antimicrobial activity against S. aureus. We used a transwell coculture system to separate the two bacterial cultures. Transcriptional profiling revealed downregulated of genes in the arc operon, the pur operon, the mnh family proteins, and cap family proteins and upregulations in the arg operon and the ahp opeorn. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30817

8 Samples

Download data: CSV, TSV

(Submitter supplied) Perhaps the most pivotal feature contributing to Staphylococcus aureus pathogenicity is the production of a wealth of virulence factors such as secreted toxins, adhesive proteins, and factors that aid in host immune evasion. The abundance and activity of these factors is tightly regulated by a multitude of effectors, including two-component systems, alternative sigma factors, DNA binding transcription factors, and regulatory RNAs. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28116

2 Samples

Download data: XLSX

(Submitter supplied) Staphylococcus aureus is a human commensal bacterium and opportunistic pathogen. Chronicity of S. aureus infection has been linked to bacterial survival within host cells including macrophages. Bacteria recovered from the intracellular milieu often form small colony variants (SCV) which are growing slowly, show reduced virulence factor production and are more resistant to antibiotics. Branched chain amino acids (BCAA) are an important class of nutrients for S. more...

Organism:

Homo sapiens; Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24034 GPL33533

12 Samples

Download data: CSV, XLSX

(Submitter supplied) To identify new genetic elements required for S.aureus pathogenesis, we performed a transposon sequencing in the context of acute murine penumonia. We screened conditionally essential genes identified by Tn-seq and confirmed 6 previously uncharacterized genes were important during infection. As further study, we performed RNA-seq to identify uncharacterized genes.

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27158

21 Samples

Download data: XLSX

(Submitter supplied) The agr quorum-sensing system clearly links Staphylococcus aureus metabolism to virulence, but little is known about how agr alters metabolism to affect cell survival during severe stress. Recently, we reported that agr activity increases survival of bacteria during treatment with lethal concentrations of H2O2, a crucial host defense against S. aureus.  Here we report that protection by agr extends to growth resumption during the exit from stationary phase. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27158

12 Samples

Download data: TSV

(Submitter supplied) The agr quorum-sensing system clearly links Staphylococcus aureus metabolism to virulence, but little is known about how agr alters metabolism to affect cell survival during severe stress. Recently, we reported that agr activity increases survival of bacteria during treatment with lethal concentrations of H2O2, a crucial host defense against S. aureus.  Here we report that protection by agr extends to growth resumption during the exit from stationary phase. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27158

6 Samples

Download data: TSV

(Submitter supplied) Regulation of gene activity during the cell cycle is fundamental to bacterial replication but is challenging to study in unperturbed, asynchronous bacterial populations. Using single cell RNA-sequencing of heterogeneous Staphylococcus aureus populations, we uncovered a global gene expression pattern dominated by chromosomal position. We show that this pattern results from the effect of DNA replication on gene expression, and in Escherichia coli, changes under different growth rates and modes of replication. more...

Organism:

Bacillus subtilis; Escherichia coli; Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24109 GPL24034 GPL21222

88 Samples

Download data: TXT