GEO DataSets

(Submitter supplied) To better understand host/phage interactions and the genetic bases of phage resistance in a model system relevant to potential phage therapy, we isolated several spontaneous mutants of the USA300 S. aureus clinical isolate NRS384 that were resistant to phage K. Six of these had a single missense mutation in the host rpoC gene, which encodes the RNA polymerase beta prime subunit. To examine the hypothesis that the mutations in the host RNA polymerase affect the transcription of phage genes, we performed RNA-seq analysis on total RNA samples collected from NRS384 wild-type (WT) and rpoC G17D mutant cultures infected with phage K, at different time points after infection. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27158

56 Samples

Download data: XLSX

(Submitter supplied) Peracetic acid (PAA), a strong oxidizing agent, has been widely used as a disinfectant in food processing settings as it does not produce harmful chlorinated by-products. In the present study, the transcriptional response of Listeria monocytogenes to 2.5 ppm of PAA was assessed using RNA-sequencing (RNA-seq). Our analysis revealed 12 differentially expressed genes, of which 9 were up-regulated (ohrR, ohrA, rpsN, lmo0637, lmo1973, fur, lmo2492, zurM, and lmo1007), and 3 were down-regulated (argG, lmo0604, lmo2156) in PAA treated samples compared to the control samples. more...

Organism:

Listeria monocytogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27107

18 Samples

Download data: TAB

(Submitter supplied) Listeria monocytogenes is a ubiquitous and psychrophilic foodborne pathogen commonly found in raw materials, ready to eat products and food environments. It was previously demonstrated that L. monocytogenes can grow faster at low temperature when unsaturated fatty acids (UFA) are present in its environment. In this study, we used comparative gene expression profiling of RNA-sequencing data to understand the impact of UFA on the behavior and cold adaptation of L. more...

Organism:

Listeria monocytogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26477

12 Samples

Download data: TXT

(Submitter supplied) Like other functional RNAs, ribozymes contain a conserved catalytic center supported by peripheral domains that vary among ribozyme sub-families. To understand how core-peripheral interactions contribute to ribozyme fitness, we compared the cleavage kinetics of all single base substitutions at 152 sites across the Bacillus subtilis glmS ribozyme by high-throughput sequencing (ClvSeq). The in vitro activity map mirrored phylogenetic sequence conservation in glmS ribozymes, indicating that biological fitness reports all biochemically important positions. more...

Organism:

Bacillus subtilis

Type:

Other

Platform:

GPL29318

12 Samples

Download data: TXT

(Submitter supplied) Pathogen-host competition for manganese and intricate immunostimulatory pathways severely attenuates the efficacy of antibacterial immunotherapy against biofilm infections associated with orthopaedic implants. Herein, we introduce an unprecedented spatiotemporal sono-metalloimmunotherapy (SMIT) strategy aimed at efficient biofilm ablation by custom design of ingenious biomimetic metal-organic framework (PCN-224)-coated MnO2-hydrangea nanoparticles (MnPM) as a metalloantibiotic. more...

Organism:

Staphylococcus aureus; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27158 GPL24247

15 Samples

Download data: TXT, XLSX

(Submitter supplied) Thiosemicarbazone R91 targets drug-resistant S. aureus by inducing copper and oxidative stress

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28116

6 Samples

Download data: XLSX

(Submitter supplied) In a previous study we used RNA-seq to identify cellular stresses related to the overexpression of xylanase XynA, and found that upregulation of the CtsR regulon improves the yield of XynA production in B. subtilis. In this study, we compared the transcriptomes of B. subtilis cells overexpressing either the xylanase XynA or the heterologous amylase AmyM, to identify general and enzyme-specific stress responses. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL28092

16 Samples

Download data: FASTA, GFF3, XLSX

(Submitter supplied) In this study we compare logrithmically grown Staphylococcus aureus SAUSA300 wildtype to a transposon mutant that is disrupted in bshC, the third step in bacillithiol biosynthesis using RNASeq to identify novel pathways where bacillithiol may be involved.

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18481

4 Samples

Download data: TXT, XLSX

(Submitter supplied) Staphylococcus aureus is a major human pathogen of the skin. The global burden of diabetes is high, with S. aureus being a major complication of diabetic wound infections. We investigated how the diabetic environment influences S. aureus skin infection and observed an increased susceptibility to infection in mouse models of both type I and type II diabetes. A dual gene expression approach was taken to investigate transcriptional alterations in both the host and bacterium after infection. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24034

8 Samples

Download data: XLS

(Submitter supplied) Bacteria have developed multiple strategies, such as sporulation, to cope with environmental stress. Non-sporulating bacteria, however, may “hibernate” into a so-called viable but non-culturable (VBNC) state, where they are no longer able to grow in standard culture media and thus become undetectable by conventional growth-based methods. VBNC pathogens pose a significant risk for human and animal health as they can “wake up” back into a vegetative and virulent state. more...

Organism:

Listeria monocytogenes EGD-e

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33865

6 Samples

Download data: TSV

(Submitter supplied) Interrogating Staphylococcus aureus transcriptional changes in the presence or absence of glycosaminoglycans, specifically heparin.

Organism:

Staphylococcus aureus subsp. aureus NCTC 8325

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33368

12 Samples

Download data: CSV

(Submitter supplied) Staphylococcus aureus is a pulmonary pathogen associated with substantial human morbidity and mortality. As vaccines targeting virulence determinants have failed to be protective in humans, other factors are likely involved in pathogenesis. Here we analysed transcriptomic responses of human clinical isolates of S. aureus from initial and chronic infections. We observed upregulated collagenase and proline transporter gene expression in chronic infection isolates. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26273

8 Samples

Download data: CSV, TXT

(Submitter supplied) Staphylococcus aureus is responsible for a substantial number of invasive infections globally each year. These infections are problematic because they are frequently recalcitrant to antibiotic treatment. Antibiotic tolerance, the ability of bacteria to persist despite normally lethal doses of antibiotics, contributes to antibiotic treatment failure in S. aureus infections. To understand how antibiotic tolerance is induced, S. more...

Organism:

Staphylococcus aureus

Type:

Other

Platform:

GPL19006

21 Samples

Download data: WIG, XLSX

(Submitter supplied) The glycopeptide vancomycin is a drug of choice for the treatment of severe non-gastrointestinal infections with members of Bacillus cereus sensu lato. Recently, sporadic detection of vancomycin resistant phenotypes emerged, mostly for agar diffusion testing. The food packaging isolate BC70 displayed a pseudo-resistant phenotype for vancomycin in both Etest and disk diffusion. In this work, we used RNA-Seq on the nanopore platform to study differentially expressed genes in BC70 cells, which were able to actively move into the inhibition zone during vancomycin susceptibility testing using Etest and therefore appeared to be resistant. more...

Organism:

Bacillus cereus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34081

4 Samples

Download data: CSV

(Submitter supplied) Staphylococcus aureus (Sa) and Acinetobacter baumannii (Ab) are frequently co-isolated from polymicrobial infections that are severe and recalcitrant to therapy. Here, we apply a combination of wet-lab experiments and in silico modeling to unveil the intricate nature of the Ab/Sa interaction using both, representative laboratory strains and strains co-isolated from clinical samples. This comprehensive methodology allowed uncovering Sa's capability to exert a partial interference on Ab by the expression of phenol-soluble modulins. more...

Organism:

Acinetobacter baumannii A118; Staphylococcus aureus subsp. aureus USA300

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34012 GPL29525

16 Samples

Download data: TXT, XLSX

(Submitter supplied) To investigate the rapid adaptation mechanism of Bacillus thuringiensis in an alkaline environment, we have employed whole genome microarray expression profiling as a discovery platform to identify the difference of gene expression between normal condition and alkaline condition.

Organism:

Bacillus thuringiensis

Type:

Expression profiling by array

Platform:

GPL17384

6 Samples

Download data: TXT

(Submitter supplied) MS2-affinity purification coupled with RNA sequencing (MAPS) reveals S. aureus RsaG sRNA targetome. Affinity purification of in vivo regulatory complexes coupled with high throughput RNA sequencing methodology or MAPS standing for “MS2 affinity purification coupled to RNA".

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19006

4 Samples

Download data: XLSX

(Submitter supplied) Listeria monocytogenes causes listeriosis, an infectious and potentially fatal disease of animals and humans. A diverse network of transcriptional regulators, including LysR-type catabolite control protein C (CcpC), is critical for the survival of L. monocytogenes and its ability to transition into the host environment. In this study, we explored the physiological and genetic consequences of deleting ccpC and the effects of such deletion on the ability of L. more...

Organism:

Listeria monocytogenes serotype 4b str. F2365

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34483

9 Samples

Download data: TXT

(Submitter supplied) Methicillin-resistant Staphylococcus aureus (MRSA) is a major threat to human health. Rather than depend on creating new antibiotics (to which bacteria will eventually become resistant), we are employing antibiotic adjuvants that potentiation existing antibiotics. Based on our previous work, loratadine, the FDA-approvide antihistamine, effectively potentiates cell-wall active antibiotics in multiple strains of MRSA. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27158

18 Samples

Download data: XLSX

(Submitter supplied) In nature, bacteria often survive in a stationary state, with low metabolic activity. Phages use the metabolic machinery of the host cell to replicate and, therefore, their efficacy against non-dividing cells is usually limited. Nevertheless, it was previously shown that the Staphylococcus epidermidis phage SEP1 has the remarkable capacity to actively replicate in stationary-phase cells, reducing their numbers. more...

Organism:

Staphylococcus epidermidis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30249

24 Samples

Download data: XLSX