Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Phenotype and RNA-Seq-Based Transcriptome Profiling of Staphylococcus aureus biofilms in response to Tea tree oil

ABSTRACT: RNA sequencing (RNA-Seq) was used in our study to elucidate the mechanism of Tea tree oil (TTO) as a potential antibacterial agent to evaluate differentially expressed genes and functional network analysis in S. aureus ATCC 29213 biofilms. Staphylococcus aureus biofilm cells were exposed for 60 minutes to TTO at concentration of 1/2ÃMBIC (1 mg/ml).2 samples including 2 control samples are analyzed.

ORGANISM(S): Staphylococcus aureus

SUBMITTER: Na Guo

PROVIDER: E-GEOD-85787 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Global transcriptional profiling of Staphylococcus aureus treated with cryptotanshinone

Project description:Staphylococcus aureus (S. aureus) is an important human and animal pathogen, multiply resistant strains are increasingly widespread, new agents are needed for the treatment of S. aureus. Cryptotanshinone, a natural plant product, has potent antimicrobial activity against S. aureus. We employed Affymetrix Staphylococcus aureus GeneChipsTM arrays to investigate the global transcriptional profiling of Staphylococcus aureus ATCC25923 treated with cryptotanshinone. Keywords: gene expression array-based, count Staphylococcus aureus cells were exposed for 45 minutes to cryptotanshinone at concentration of 2 Âµg/ml (1/2Ã? MIC), 6 samples including 3 control samples are analyzed.

2010-05-18 | E-GEOD-13203 | biostudies-arrayexpress

Global transcriptional profiling of Staphylococcus aureus treated with rhein

Project description:Staphylococcus aureus is one of the most important pathogens in humans and animals, multiply resistant strains are increasingly widespread, new agents are needed for the treatment of S. aureus. Rhein, a natural plant product, has potential antimicrobial activity against Staphylococcus aureus. We employed Affymetrix Staphylococcus aureus GeneChipsTM arrays to investigate the global transcriptional profiling of Staphylococcus aureus ATCC25923 treated with rhein. Results provided insight into mechanisms involved in rhein - Staphylococcus aureus interactions. Keywords: rhein response Staphylococcus aureus cells were exposed for 45 minutes to rhein at concentration of 8 Âµg/ml (1/2Ã MIC), 6 samples including 3 control samples are analyzed.

2010-06-10 | E-GEOD-8135 | biostudies-arrayexpress

Phenotype and expression profile analysis of Staphylococcus aureus biofilms and planktonic cells in response to Licochalcone A

Project description:Staphylococcus aureus (S. aureus) is one of the most important pathogens in humans and animals. The formation of S. aureus biofilm is considered an important mechanism of antimicrobial resistance. Therefore, finding effective drugs against the biofilm produced by S. aureus has been a high priority. Licochalcone A, a natural plant product, was reported to have antibacterial activities and showed good activity against all 21 tested strains of S. aureus biofilm and planktonic cells. To detect the possible molecular mechanism of Licochalcone A against S. aureus biofillm or planktonic cells, Affymetrix GeneChips were used to determine the global comparative transcription of S. aureus biofilm and planktonic cells triggered by treatment with sub-bactericidal and sub-inhibitory concentrations of Licochalcone A, respectively. Staphylococcus aureus planktonic cells and biofilm were exposed for 60 minutes to Licochalcone A at concentration of 2 M-NM-<g/ml (1/2M-CM-^W MIC) and 64 M-NM-<g/ml (4M-CM-^W MIBC), respectively. 4 samples including 4 control samples are analyzed.

2014-07-01 | E-GEOD-58938 | biostudies-arrayexpress

Global transcriptional profiling of Staphylococcus aureus treated with sodium houttuyfonate

Project description:Staphylococcus aureus (S. aureus) is an important human and animal pathogen, multiply resistant strains are increasingly widespread, new agents are needed for the treatment of S. aureus. sodium houttuyfonate has potent antimicrobial activity against S. aureus. We employed Affymetrix Staphylococcus aureus GeneChipsTM arrays to investigate the global transcriptional profiling of Staphylococcus aureus ATCC25923 treated with sodium houttuyfonate. Keywords: gene expression array-based, count Staphylococcus aureus cells were exposed for a certain to sodium houttuyfonate at certain concentration, 6 samples including 3 control samples are analyzed.

2010-05-18 | E-GEOD-13233 | biostudies-arrayexpress

Global transcriptional profiling of Staphylococcus aureus treated with magnolol

Project description:Staphylococcus aureus (S. aureus) is an important human and animal pathogen, multiply resistant strains are increasingly widespread, new agents are needed for the treatment of S. aureus. magnolol has potent antimicrobial activity against S. aureus. We employed Affymetrix Staphylococcus aureus GeneChipsTM arrays to investigate the global transcriptional profiling of Staphylococcus aureus ATCC25923 treated with magnolol. Keywords: gene expression array-based, count Staphylococcus aureus cells were exposed for a certain time to magnolol at a certain concentration, 6 samples including 3 control samples are analyzed.

2010-05-18 | E-GEOD-13236 | biostudies-arrayexpress

Global transcriptional profiling of Staphylococcus aureus treated with eugenol

Project description:Staphylococcus aureus (S. aureus) is an important human and animal pathogen, multiply resistant strains are increasingly widespread, new agents are needed for the treatment of S. aureus. eugenol, a natural plant product, has potent antimicrobial activity against S. aureus. We employed Affymetrix Staphylococcus aureus GeneChipsTM arrays to investigate the global transcriptional profiling of Staphylococcus aureus ATCC25923 treated with eugenol. Keywords: gene expression array-based, count Staphylococcus aureus cells were exposed for 45 minutes to eugenol at concentration of 250µg/ml (1/2× MIC), 2 samples including 1 control samples are analyzed.

2007-08-10 | E-GEOD-8735 | biostudies-arrayexpress

Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus

Project description:In Staphylococcus aureus, hundreds of small regulatory or small RNAs (sRNAs) have been identified, yet this class of molecule remains poorly understood and severely understudied. sRNA genes are typically absent from genome annotation files, and as a consequence, their existence is often overlooked, particularly in global transcriptomic studies. To facilitate improved detection and analysis of sRNAs in S. aureus, we generated updated GenBank files for three commonly used S. aureus strains (MRSA252, NCTC 8325, and USA300), in which we added annotations for >260 previously identified sRNAs. These files, the first to include genome-wide annotation of sRNAs in S. aureus, were then used as a foundation to identify novel sRNAs in the community-associated methicillin-resistant strain USA300. This analysis led to the discovery of 39 previously unidentified sRNAs. Investigating the genomic loci of the newly identified sRNAs revealed a surprising degree of inconsistency in genome anno- tation in S. aureus, which may be hindering the analysis and functional exploration of these elements. Finally, using our newly created annotation files as a reference, we perform a global analysis of sRNA gene expression in S. aureus and demonstrate that the newly identified tsr25 is the most highly upregulated sRNA in human serum. This study provides an invaluable resource to the S. aureus research community in the form of our newly generated annotation files, while at the same time presenting the first examination of differential sRNA expression in pathophysiologically relevant conditions. Four RNAseq data sets in total. Each sample was generated by pooling three independent biological replicate RNA preps

2016-01-05 | E-GEOD-74936 | biostudies-arrayexpress

Global transcriptome analysis of Staphylococcus aureus biofilms in response to innate immune cells

Project description:S. aureus biofilms are associated with the organism's ability to cause disease. Biofilm associated bacteria must cope with the host's innate immune system. We used commercially available Affymetrix S. aureus GeneChips to compare the gene expression properties of 4 and 6 day established biofilms following short (1 hr)- and long (24 hr)- term exposure to macrophages and neutrophils. S. aureus strain USA300 LAC biofilms where formed for 4 or 6 days. Established biofilms were then exposed to macrophages for 1 or 24 hr. Alternatively, biofilms were exposed to neutrophils for 1 or 4 hr. Total bacterial RNA was isolated and subjected to GeneChip hybridization and analysis. We sought to determine the regulatory effects of Macrophages and Neutrophils on established S. aureus biofilms.

2013-12-01 | E-GEOD-50675 | biostudies-arrayexpress

Characterizing the transcriptional adaptation of Staphylococcus aureus to stationary phase growth

Project description:Staphylococcus aureus is an important human pathogen that causes life-threatening infections, and is resistant to the majority of our antibiotic arsenal. This resistance is complicated by the observation that most antibacterial agents target actively growing cells, thus, proving ineffective against slow growing populations, such as cells within a biofilm or in stationary phase. Recently, our group generated updated genome annotation files for S. aureus that not only include protein-coding genes but also regulatory and small RNAs. As such, these annotation files were used to perform a transcriptomic analysis in order to understand the metabolic and physiological changes that occur during transition from active growth to stationary phase; with a focus on sRNAs. We observed â¼24% of protein-coding and 34% of sRNA genes displaying changes in expression by â¥3-fold. Collectively, this study adds to our understanding of S. aureus adaptation to nutrient-limiting conditions, and sheds new light onto the contribution of sRNAs to this process. Bacterial cells were grown in TSB medium at 37Â°C with shaking for 3h (exponential growth phase) or 16h (stationary growth phase).

2016-05-18 | E-GEOD-77242 | biostudies-arrayexpress

Tea tree oil induced transcriptional alterations in Staphylococcus aureus

Project description:S. aureus and MRSA are susceptible to TTO and are therefore targeted in nascent TTO clinical trails. We now report the alterations in the transcriptome of a S. aureus exposed to a growth inhibitory concentration of TTO. These efforts have uncovered additional mechanisms by which this membrane active antimicrobial substance inhibits bacterial growth. Four hybridizations, including a biological replicate and a dye-swap experiment for each replicate was carried out. LOWESS normalization was performed on the raw data to correct for dye-bias. Statistical analysis was performed using a significance analysis of microarrays (SAM, MultiExperiment Viewer, ver. 4.0) unpaired contrast. A d-statistic was calculated for each gene based on repeated permutations, and a false discovery rate FDR of 0.01 was used to assign a critical cutoff for significance.

2012-04-25 | E-GEOD-31554 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data