GEO DataSets

(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) Guanidine DNA quadruplex (G4-DNA) structures convey a distinctive layer of epigenetic information that is critical for the regulation of key biological activities and processes as genome transcription regulation, replication and repair. Despite several works that have been published recently, the information regarding their role and possible use as therapeutic drug targets in bacteria is still scarce. more...

Organism:

Escherichia coli; Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17452 GPL14548

8 Samples

Download data: RPKM

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

Organism:

Staphylococcus aureus

Type:

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

Platforms:

GPL18481 GPL17452

19 Samples

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(Submitter supplied) Here, we use a panel of defined walKR mutants and functional genomics including ChIP-seq to confirm a high-resolution consensus WalR DNA-binding motif and characterise a 61-gene direct regulon

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17452

6 Samples

Download data: CSV

(Submitter supplied) Staphylococcus aureus (S. aureus) is a gram-positive bacterium that causes a wide range of diseases. Terpinen-4-ol is a monoterpene component contained in most plant essential oils with good antibacterial activity. In this study, terpinen-4-ol effectively inhibited 13 strains of S. aureus, and effectively inhibited the biofilm of MRSA. Metabolomics and transcriptomics were used to elucidate changes in MRSA cells exposed to terpinen-4-ol. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17452

6 Samples

Download data: TXT

(Submitter supplied) Here we report a direct tRNA sequencing protocol and software to simultaneously examine the composition and biological activity of naturally occurring microbial communities. Our analysis of mouse gut microbiome with tRNA-seq and 16S ribosomal RNA gene amplicons revealed comparable microbial community structures, and additional physiological insights into the microbiome through tRNA abundance and modifications.

Organism:

Bacillus subtilis; mouse gut metagenome; Barnesiella viscericola; Escherichia coli; Staphylococcus aureus

Type:

Non-coding RNA profiling by high throughput sequencing

6 related Platforms

28 Samples

Download data: TXT, XLSX

(Submitter supplied) Staphylococcus aureus is a major opportunistic pathogen and notable efforts are currently under way to develop new methods to combat staphylococcal infections. It is becoming increasingly clear that understanding the ecology of pathogenic bacteria is important to design improved disinfection and therapeutic strategies. Like many microbes, S. aureus commonly forms biofilms on various biotic and abiotic surfaces. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17452

6 Samples

Download data: TXT

(Submitter supplied) Endonucleolytic cleavage within polycistronic mRNAs can lead to differential stability and discordant abundance among co-transcribed genes. RNase Y, the major endonuclease for mRNA decay in Bacillus subtilis, was originally identified for its cleavage activity towards the cggR-gapA operon, an event that differentiates the expression of a glycolytic enzyme from its transcriptional regulator. A three-protein Y-complex (YlbF, YmcA, and YaaT) was recently identified that is also required for this cleavage in vivo, raising the possibility that it is an accessory factor acting to regulate RNase Y. more...

Organism:

Bacillus subtilis; Staphylococcus aureus

Type:

Other

Platforms:

GPL17452 GPL18561

16 Samples

Download data: WIG

(Submitter supplied) The Staphylococcus aureus strain Newman uses the dithiol-containing repressor CstR to sense sulfide stress via reactive sulfur species (RSS), allowing transcription of a mitochondrial-like sulfide oxidation system, the core of which is genetically linked to methicillin resistance determinants in MRSA strains. The cytoplasm maintains an excess of reduced relative to oxidized low molecular weight (LMW) thiols that are protective against oxidative stress and transition metal (Zn, Cd and Cu) toxicity, buffering these ions to low “free” concentrations via formation of coordination complexes. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19006 GPL17452

18 Samples

Download data: TXT

(Submitter supplied) Phage-derived lytic proteins are a promising alternative to conventional antimicrobials. One of their most interesting properties is that they do not readily select for resistant strains, which is likely due to the fact that their targets are essential for the viability of the bacterial cell. Moreover, genetic engineering allows the design of new "tailor-made" proteins that may exhibit improved antibacterial properties. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17452

6 Samples

Download data: TXT

(Submitter supplied) An important lesson from the war on pathogenic bacteria has been the need to understand the physiological responses and evolution of natural microbial communities. Bacterial populations in the environment are generally forming biofilms subject to some level of phage predation. These multicellular communities are notoriously resistant to antimicrobials and, consequently, very difficult to eradicate. This has sparked the search for new therapeutic alternatives, including phage therapy. This study demonstrates that S. aureus biofilms formed in the presence of a non-lethal dose of phage phiIPLA-RODI exhibit a unique physiological state that could potentially benefit both the host and the predator. Thus, biofilms formed under phage pressure are thicker and have a greater DNA content. Also, the virus-infected biofilm displayed major transcriptional differences compared to an untreated control. Significantly, RNA-seq data revealed activation of the stringent response, which could slow down the advance of the bacteriophage within the biofilm. The end result would be an equilibrium that would help bacterial cells to withstand environmental challenges, while maintaining a reservoir of sensitive bacterial cells available to the phage upon reactivation of the dormant carrier population.

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17452

6 Samples

Download data: TXT

(Submitter supplied) Background Bacteria rely on efficient gene regulatory mechanisms to switch between genetic programs when they are facing new environments. Although this regulation can occur at many different levels, one of the key steps is the initiation of transcription. Identification of the first nucleotide transcribed by the RNA polymerase is therefore essential to understand the underlying regulatory processes, since this provides insight on promoter strength and binding sites for transcriptional regulators, and additionally reveals the exact 5' untranslated region of the transcripts, which often contains elements that regulate translation. more...

Organism:

Acinetobacter baumannii; Staphylococcus aureus; Staphylococcus epidermidis; Klebsiella aerogenes

Type:

Expression profiling by high throughput sequencing; Other

4 related Platforms

30 Samples

Download data: TSV

(Submitter supplied) We examined the differential gene expression of Staphylococcus epidermidis and Staphylococcus epidermidis in dual species biofilms. Therefore, we performed RNA-Seq on single and dual species biofilms and we compared the gene expression levels in dual species biofilms to those in single species biofilms.

Organism:

Staphylococcus epidermidis; Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21653 GPL17452 GPL21652

9 Samples

Download data: XLSX

(Submitter supplied) It remains unclear how the bacterial populations which colonise many healthy humans occasionally give rise to severe disease. Staphylococcus aureus represents one such population. Here we describe mutations in invasive S. aureus which arose during human colonisation and inactivated rsp, a transcription factor. RNA-Seq was used to generate mRNA profiles of genes controlled by rsp.

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17452

12 Samples

Download data: TXT

(Submitter supplied) We sequenced a total of 16 cDNA libararies derived from fragmented total mRNA and ribosome protected mRNAs from S. aureus hpf mutant (NE838) and its parental strain JE2 grown in tryptic soy broth (TSB) or minimal medium (MM). The data represented 2 independent biological replicates.

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17452

16 Samples

Download data: TXT

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of gene regulon. The goal of this study is to investigate the genes regulated by Rsp in MRSA BD02-25 Methods: mRNA profiles of wild-type (WT) and Rsp knockout (△Rsp) MRSA at mid-logarithmic growth phase (4h) were generated by deep sequencing, respectively in duplicate samples, using the Hiseq2000 (Illumina, CA) sequencer. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17452

4 Samples

Download data: TXT

(Submitter supplied) Little is known about regulation of gene activity of the major pathogen Staphylococcus aureus during actual human infection. Here we characterize the transcriptome using deep RNA sequencing and the metabolome using NMR of S. aureus infected joint fluid derived from an acute human prosthetic joint infection, and compare them with the genome, transcriptome and metabolome of an isolate obtained from the sample grown in vitro (LB medium). more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17452

4 Samples

Download data: TXT

(Submitter supplied) Staphylococcus aureus is a gram-positive cocci and an important human commensal bacteria and pathogen. S. aureus infections are increasingly difficult to treat because of the emergence of highly resistant MRSA (Methicillin-resistant S. aureus) strains. Here we present a method to study differential gene expression in S. aureus using high-throughput RNA-sequencing (RNA-seq). We use RNA-seq to examine the differential gene expression in S. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17452

3 Samples

Download data: WIG