Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

56 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of coding RNA of Staphylococcus aureus COL wild type strain before and after 30 min of exposure to 176 μM neutrophil-derived oxidant hypothiocyanous acid (HOSCN) during exponential phase of an OD540 of 0.5 in LB medium

ABSTRACT: Staphylococcus aureus COL wild type strain was cultivated in LB medium in 3 biological replicates and harvested at an OD500 of 0.5 before (as control) and at 30 min after exposure to 1176 μM neutrophil-derived oxidant hypothiocyanous acid (HOSCN) stress. Cells were disrupted in 3 mM EDTA/ 200 mM NaCl lysis buffer with a Precellys24 ribolyzer followed by RNA isolation using the acid phenol extraction protocol as described. The RNA quality was approved by Trinean Xpose (Gentbrugge, Belgium) and the Agilent RNA Nano 6000 kit using an Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina (San Diego, CA, USA) was applied to prepare the cDNA libraries. The cDNAs were sequenced paired end on an NextSeq 500 (San Diego, CA, USA) using 75 bp read length and a minimum sequencing depth of 8 million reads per library. The paired end cDNA reads were mapped to the Staphylococcus aureus COL genome sequence (accession number CP000046) using bowtie2 v2.2.7 (Langmead and Salzberg, 2012) with default settings for paired-end read mapping. All mapped sequence data were converted from SAM to BAM format with SAMtools v1.3 (Li et al., 2009) and imported to the software ReadXplorer v.2.2 (Hilker et al., 2016).

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Staphylococcus aureus

SUBMITTER: Tobias Busche

PROVIDER: E-MTAB-13314 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of coding RNA of Staphylococcus aureus USA300 wild type strain before and after 30 min of exposure to 1.5 mM in RPMI HOCl stress during the log phase in RPMI media

Project description:Staphylococcus aureus USA300 wild type strain was cultivated in RPMI medium in 3 biological replicates and harvested at an OD500 of 0.5 before (as control) and at 30 min after exposure to 1.5 mM in RPMI HOCl stress. Cells were disrupted in 3 mM EDTA/ 200 mM NaCl lysis buffer with a Precellys24 ribolyzer followed by RNA isolation using the acid phenol extraction protocol as described. The RNA quality was approved by Trinean Xpose (Gentbrugge, Belgium) and the Agilent RNA Nano 6000 kit using an Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina (San Diego, CA, USA) was applied to prepare the cDNA libraries. The cDNAs were sequenced paired end on an Illumina HiSeq 1500 (San Diego, CA, USA) using 70 and 75 bp read length and a minimum sequencing depth of 10 million reads per library. The paired end cDNA reads were mapped to the Staphylococcus aureus USA300 genome sequence (accession number FPR3757_CP255) using bowtie2 v2.2.7 (Langmead and Salzberg, 2012) with default settings for paired-end read mapping. All mapped sequence data were converted from SAM to BAM format with SAMtools v1.3 (Li et al., 2009) and imported to the software ReadXplorer v.2.2 (Hilker et al., 2016).

2023-09-30 | E-MTAB-13313 | biostudies-arrayexpress

RNA-seq of coding RNA of Staphylococcus aureus wild type strain before and after 30 min of exposure to 13 mM itaconic acid stress reveals adaption to the immunometabolite itaconate by inducing acid and oxidative stress responses

Project description:S. aureus COL was cultivated in RPMI medium in 3 biological replicates and harvested at an OD500 of 0.5 before (as control) and at 30 min after exposure to 13 mM itaconic acid stress. Cells were disrupted in 3 mM EDTA/ 200 mM NaCl lysis buffer with a Precellys24 ribolyzer followed by RNA isolation using the acid phenol extraction protocol as described. The RNA quality was approved by Trinean Xpose (Gentbrugge, Belgium) and the Agilent RNA Nano 6000 kit using an Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina (San Diego, CA, USA) was applied to prepare the cDNA libraries. The cDNAs were sequenced paired end on an Illumina HiSeq 1500 (San Diego, CA, USA) using 70 and 75 bp read length and a minimum sequencing depth of 10 million reads per library.

2023-09-10 | E-MTAB-13287 | biostudies-arrayexpress

RNA-seq of coding RNA of Streptococcus pneumoniae D39 after FCS addition

Project description:Streptococcus pneumoniae (S.p.) is the most common causative agent of community-acquired pneumonia worldwide. A key pathogenic mechanism that exacerbates severity of disease is the disruption of the alveolo-capillary barrier. However, the specific virulence mechanisms responsible for this in the human lung are not yet fully understood. RNA sequencing of Streptococcus pneumoniae transcriptome under infection media conditions, but without the presence of lung tissue, representing anon-host-infection scenario FCS+/- was analyzed,. RNA isolation was performed using an acidic phenol-chloroform extraction protocol (Wetzstein et al., 1992). After DNase-I treatment (Zymo Research, Germany), the RNA quality was checked by Trinean Xpose (Gentbrugge, Belgium) and the Agilent RNA Nano 6000 kit using an Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). For RNA-seq transcriptomics, Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina (San Diego, CA, United States) was applied to prepare the cDNA libraries. The cDNAs were sequenced paired end on an Illumina HiSeq 1500 (San Diego, CA, United States) using 70 and 75 bp read length and a minimum sequencing depth of 10 million reads per library.

2023-11-30 | E-MTAB-13533 | biostudies-arrayexpress

RNA-seq of coding RNA of Actinoplanes sp. SE50/110 to analyze gene function of alternative sigma factor gene ACSP50_0507

Project description:Cultivation in maltose minimal media and sampling at different time point (t2 = 96h; t3=118h; t4 = 142h; t5 = 166h) of Actinoplanes sp. SE50/110 empty vector control and Actinoplanes sp. SE50/110 ACSP50_0507 overxepression mutant. RNAseq material and methods

2024-07-22 | E-MTAB-13644 | biostudies-arrayexpress

RNAseq of Staphylococcus aureus wildtype and ppGpp0 mutant reveals rolen of alarmon (p)ppGpp confering tolerance to oxidative stress and antibiotics during the stationary phase in Staphylococcus aureus

Project description:RNAseq of coding RNA in Staphylococcus aureus wildtype and ppGpp0 mutant shows transcription of the Fe-storage ferritin (ftnA) and miniferritin (dps) was elevated in the ppGpp0 mutant, while Fur-regulated iron transporters for uptake of heme or siderophores were repressed, including the isdABCDEFG, sirABC and sstADBCD-operons. Together these results indicate that (p)ppGpp confers tolerance to ROS and antibiotics during the stationary phase by down-regulation of internal iron levels to prevent ROS formation.

2020-08-31 | E-MTAB-9368 | biostudies-arrayexpress

Comparative secretome analysis of Staphylococcus aureus strains with different within-herd intramammary infection prevalence

Project description:This investigation reports a differential proteomic analysis of the secretome of six S. aureus strains belonging to two genotypes with opposite within-herd prevalence, GTB (high) and GTS (low), corresponding to sequence types (ST) 8 and 398, respectively. Total proteins released in the growth medium were subjected to high-resolution tandem mass spectrometry and differential analysis with Proteome Discoverer by label-free approach. Here, we reported both the characterization of secretome proteins and a panel of differential proteins specific of S. Aureus depending on high or low within-herd prevalence. GTB/ST8 (High) released more immunoglobulin-binding proteins, complement and antimicrobial peptide inhibitors, enterotoxins, and metabolic enzymes, while GTS/ST398 (Low) released more leukocidins, hemolysins, lipases, and peptidases. Furthermore, GTB/ST8 (High) released the von Willebrand factor protein, staphylokinase, and clumping factor B, while GTS/ST398 (Low) released the staphylococcal coagulase and clumping factor A. In conclusion, our results provide an in-depth characterization of secretome proteins of the three S. aureus GTB/ST8 and three GTS/ST398 strains with high and low within-herd prevalence. We describe the role of extracellular proteins in S. Aureus pathogenesis.

2022-02-14 | PXD029571 | Pride

The garlic compound allicin causes strong disulfide stress and protein S-sulfoallylation as revealed by proteomics and transcriptomics in Staphylococcus aureus

Project description:Allicin from garlic is an antimicrobial substance that is effective against several ESKAPE pathogens, including methicillin-resistant Staphylococcus aureus (MRSA). However, the antimicrobial mode action of allicin has not been revealed in Gram-positive bacteria. Here, we have studied the changes in the transcriptome by Allicin which revealed a thiol-specific oxidative stress response in S. aureus. Using shotgun proteomics, we identified numerous proteins that were modified by protein S-sulfoallylation in S. aureus. Allicin further caused an oxidative shift in the bacillithiol (BSH) redox potential as revealed by Brx-roGFP2 biosensor measurements. In summary, our results revealed that allicin acts via sulfoallylation of Cys residues in proteins causing an impaired redox state in S. aureus.

2022-02-28 | PXD010338 | Pride

Gene expression analysis of Vancomycin resistance in Stapyloccoccus aureus strains: PA, C1 and T8.

Project description:The study aims to identify genes associated with Vancomycin resistance. Wild type and a mutant cells line were treated with antibiotic at multiple concentrations and RNA samples extracted over a two hour time course.Staphylococcus aureus strain PA is the reference for this series. Wild type and a mutant cells line were treated with antibiotic at multiple concentrations and RNA samples extracted over a two hour time course. Samples were hybridized on aminosilane coated slides with 70-mer oligos.

2011-04-08 | E-GEOD-26400 | biostudies-arrayexpress

Host Response Signature to Staphylococcus aureus alpha-Hemolysin

Project description:Staphylococcus aureus pneumonia causes significant morbidity and mortality. Alpha-hemolysin (Hla), a pore-forming cytotoxin of S. aureus, has been identified through animal models of pneumonia as a critical virulence factor that induces lung injury. In spite of considerable molecular knowledge of how this cytotoxin injures the host, the precise host response to Hla in the context of infection remains poorly understood. We employed whole-genome expression profiling of infected lung to define the host response to wild-type S. aureus compared with an Hla-deficient isogenic mutant in experimental pneumonia. These data provide a complete expression profile at four and at twenty-four hours post-infection, revealing a unique response to the toxin-expressing strain. Gene ontogeny analysis revealed significant differences in the extracellular matrix and cardiomyopathy pathways, both of which govern cellular interactions in the tissue microenvironment. Evaluation of individual transcript responses to Hla-secreting bacteria was notable for upregulation of host cytokine and chemokine genes, including the p19 subunit of interleukin-23. Consistent with this observation, the cellular immune response to infection was characterized by a prominent TH17 response to wild-type staphylococci. These findings define specific host mRNA responses to Hla-producing S. aureus, coupling the pulmonary TH17 response to the presence of this cytotoxin. Expression profiling to define the host response to a single virulence factor proved to be a valuable tool in identifying pathways for further investigation in S. aureus pneumonia. This approach may be broadly applicable to the study of bacterial toxins, defining host pathways that can be targeted to mitigate toxin-induced disease. Animals were treated with PBS, S. aureus wild-type, or S. aureus Hla-deficient isogenic mutant.

2012-05-20 | E-GEOD-38053 | biostudies-arrayexpress

Norwegian Red (NRF) cattle macrophage challenge1

Project description:In vitro challenge of bovine macrophages (derived from blood monocytes)with live bacteria of a Staphylococcus aureus strain isolated from a clinical mastitis case.

2012-01-01 | E-TABM-1133 | 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