Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

51 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of coding RNA reveals an oxidative stress response induced by the plant-derived naphthoquinone lapachol in Staphylococcus aureus

ABSTRACT: RNA-seq transcriptomics was performed using RNA of S. aureus COL in triplicate, which was grown in RPMI medium and subjected to 300 µM lapachol for 30 min. Differential gene expression analysis of 3 biological replicates was performed using DESeq2. RNA-seq transcriptome analysis reveals: lapachol causes an oxidative and quinone stress response and protein damage as shown by induction of the PerR, HypR, QsrR, MhqR, CstR and HrcA regulons. Lapachol treatment further resulted in up-regulation of the SigB and GraRS regulons, which is indicative for cell wall and general stress responses.

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Staphylococcus aureus subsp. aureus COL

SUBMITTER: Haike Antelmann

PROVIDER: E-MTAB-8691 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

The role of the quinone-sensing regulator MhqR in Staphylococcus aureus analysed by RNA-seq of coding RNA

Project description:Using RNAseq transcriptomics, we monitored the global changes in gene expression of Staphylococcus aureus COL and the ∆mhqR mutant after exposure to 45 µM methylhydroquinone (MHQ) stress. Strain cultivation was performed in RPMI1640 medium (Lonza) under vigorous agitation in triplicate at 37°C until cells have reached an optical density at 500 nm of 0.5. S. aureus cells were harvested before and 30 min after exposure to 45 µM MHQ and disrupted in 3 mM EDTA/ 200 mM NaCl lysis buffer with a Precellys24 Ribolyzer. RNA isolation was performed using the phenol-chloroform-isoamylalcohol approach. After precipitation with 3 M sodium acetate and isopropanol, the total RNA was washed with cold ethanol and the pellet was solved in sterile water. Initially RNA quality was checked by Trinean Xpose (Gentbrugge,Belgium) and Agilent RNA Nano 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). Samples contaminated with DNA were treated with DNase (Qiagen), cleaned as described above and rechecked by Xpose and Agilent Bioanalyzer. Finally RNA was free of DNA with an RNA Integrity Number (RIN) > 9 and rRNA Ratio [23s / 16s] > 1.5. Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the ribosomal RNA molecules from the isolated total RNA. Removal of rRNA was checked by Agilent RNA Pico 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). RNA was free of detectable rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina (San Diego, CA, USA) was used to prepare cDNA libraries. The resulting cDNAs were sequenced paired end on an Illumina HiSeq 1500 system (San Diego, CA, USA) using 70 bp read length.

2019-09-04 | E-MTAB-7218 | biostudies-arrayexpress

RNAseq of Staphylococcus aureus wildtype and two-Cys-type TetR repressor GbaA deletion mutant under nonstress condition

Project description:To investigate the changes in gene expression of Staphylococcus aureus COL and the gbaA deletion mutant under nonstress condition, strains were cultivated in RPMI1640 medium (Lonza) under vigorous agitation at 37°C in triplicate until cells have reached an optical density at 500 nm of 0.5. S. aureus cells were harvested and disrupted in 3 mM EDTA/ 200 mM NaCl lysis buffer with a Precellys24 Ribolyzer. RNA isolation was performed using the phenol-chloroform-isoamylalcohol approach. After precipitation with 3 M sodium acetate and isopropanol, the total RNA was washed with cold ethanol and the pellet was solved in sterile water. Initially RNA quality was checked by Trinean Xpose (Gentbrugge,Belgium) and Agilent RNA Nano 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). Samples contaminated with DNA were treated with DNase (Qiagen), cleaned as described above and rechecked by Xpose and Agilent Bioanalyzer. Finally RNA was free of DNA with an RNA Integrity Number (RIN) > 9 and rRNA Ratio [23s / 16s] > 1.5. Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the ribosomal RNA molecules from the isolated total RNA. Removal of rRNA was checked by Agilent RNA Pico 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). RNA was free of detectable rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina (San Diego, CA, USA) was used to prepare cDNA libraries. The resulting cDNAs were sequenced paired end on an Illumina HiSeq 1500 system (San Diego, CA, USA) using 70 bp read length.

2021-10-25 | E-MTAB-10887 | biostudies-arrayexpress

RNA-seq of coding RNA of Staphylococcus aureus treated with the antimicrobial coating AgXX reveals strong thiol-specific stress response and protein S-bacillithiolation in Staphylococcus aureus

Project description:Using RNAseq transcriptomics, we monitored the global changes in gene expression of Staphylococcus aureus USA300 TCH1516 after exposure to the antimicrobial coating AgXX373 (Largetec GmbH, Berlin). Strain cultivation was performed in RPMI1640 medium (Lonza) under vigorous agitation at 37°C in triplicate until cells have reached an optical density at 500 nm of 0.5. S. aureus cells were harvested before and 30 min after exposure to 4.5 µg/ml AgXX373 and disrupted in 3 mM EDTA/ 200 mM NaCl lysis buffer with a Precellys24 Ribolyzer. RNA isolation was performed using the phenol-chloroform-isoamylalcohol approach. After precipitation with 3 M sodium acetate and isopropanol, the total RNA was washed with cold ethanol and the pellet was solved in sterile water. Initially RNA quality was checked by Trinean Xpose (Gentbrugge,Belgium) and Agilent RNA Nano 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). Samples contaminated with DNA were treated with DNase (Qiagen), cleaned as described above and rechecked by Xpose and Agilent Bioanalyzer. Finally RNA was free of DNA with an RNA Integrity Number (RIN) > 9 and rRNA Ratio [23s / 16s] > 1.5. Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the ribosomal RNA molecules from the isolated total RNA. Removal of rRNA was checked by Agilent RNA Pico 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). RNA was free of detectable rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina (San Diego, CA, USA) was used to prepare cDNA libraries. The resulting cDNAs were sequenced paired end on an Illumina HiSeq 1500 system using 70 bp read length.

2019-07-04 | E-MTAB-7074 | 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

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 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 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

Project description: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).

2023-09-30 | E-MTAB-13314 | biostudies-arrayexpress

The global effect of the garlic compound Allicin on the changes in the transcriptome in Bacillus subtilis and Staphylococcus aureus USA300 analysed by RNA-seq of coding RNA

Project description:To monitor the global changes in gene expression of Staphylococcus aureus USA300 TCH1516 under exposure to the garlic compound Allicin by RNA-seq, cultivation was performed in shaking flasks in Luria Bertani (LB) medium in triplicate at 37C until cells have reached an optical density at 540nm of 2.0. Cells were harvested by centrifugation, washed with Belitsky minimal medium (BMM) and adapted to BMM for one hour before exposure to 300 M Allicin stress. S. aureus cells of 3 replicate experiments were harvested before and 30 min after exposure to 300 M Allicin and disrupted in 3 mM EDTA/ 200 mM NaCl lysis buffer with a Precellys24 Ribolyzer. RNA isolation was performed using the phenol-chloroform-isoamylalcohol approach. After precipitation with 3 M sodium acetate and isopropanol, the total RNA was washed with cold ethanol and the pellet was solved in sterile water. Initially RNA quality was checked by Trinean Xpose (Gentbrugge,Belgium) and Agilent RNA Nano 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Bblingen, Germany). Samples contaminated with DNA were treated with DNase (Qiagen), cleaned as described above and rechecked by Xpose and Agilent Bioanalyzer. Finally RNA was free of DNA with an RNA Integrity Number (RIN) > 9 and rRNA Ratio [23s / 16s] > 1.5. Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the ribosomal RNA molecules from the isolated total RNA. Removal of rRNA was checked by Agilent RNA Pico 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Bblingen, Germany). RNA was free of detectable rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina (San Diego, CA, USA) was used to prepare cDNA libraries. The resulting cDNAs were sequenced paired end on an Illumina MiSeq system (San Diego, CA, USA) using 75 bp read length.

2019-04-01 | E-MTAB-5667 | biostudies-arrayexpress

The global effect of hypochlorite stress on the changes in the transcriptome in Staphylococcus aureus USA300

Project description:To monitor the global changes in gene expression of Staphylococcus aureus USA300 TCH1516 under hypochlorite stress by RNA-seq, cultivation was performed in Luria Bertani (LB) medium in triplicate at 37C until cells have reached an optical density at 540nm of 2.0. Cells were harvested by centrifugation, washed with Belitsky minimal medium (BMM) and adapted to BMM for one hour before exposure to 150 M NaOCl stress. S. aureus cells of 3 replicate experiments were harvested before and 30 min after exposure to 150 M NaOCl and disrupted in 3 mM EDTA/ 200 mM NaCl lysis buffer with a Precellys24 Ribolyzer. RNA isolation was performed using the phenol-chloroform-isoamylalcohol approach. After precipitation with 3 M sodium acetate and isopropanol, the total RNA was washed with cold ethanol and the pellet was solved in sterile water. Initially RNA quality was checked by Trinean Xpose (Gentbrugge,Belgium) and Agilent RNA Nano 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Bblingen, Germany). Samples contaminated with DNA were treated with DNase (Qiagen), cleaned as described above and rechecked by Xpose and Agilent Bioanalyzer. Finally RNA was free of DNA with an RNA Integrity Number (RIN) > 9 and rRNA Ratio [23s / 16s] > 1.5. Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the ribosomal RNA molecules from the isolated total RNA. Removal of rRNA was checked by Agilent RNA Pico 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Bblingen, Germany). RNA was free of detectable rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina (San Diego, CA, USA) was used to prepare cDNA libraries. The resulting cDNAs were sequenced paired end on an Illumina HiSeq 1500 and MiSeq system (San Diego, CA, USA) using 50 and 75 bp read length, respectively.

2017-12-18 | E-MTAB-5666 | biostudies-arrayexpress

RNA-seq of coding RNA of Streptococcus pneumoniae D39 wild type strain before and after 30 min of exposure to sub-lethal doses of 800 µM HOCl stress during the log phase of microaerophilic grown bacteria

Project description:RNA-seq of coding RNA of Streptococcus pneumoniae D39 wild type strain before and after 30 min of exposure to sub-lethal doses of 800 µM HOCl stress during the log phase of microaerophilic grown bacteria. The S. pneumoniae D39 wild type strain was cultivated in RPMI medium and treated with thiol-reactive compound NaOCl, which dissociates in aqueous solution to hypochlorous acid (HOCl) and hypochlorite (OCl−) - the concentration of HOCl was determined by absorbance measurements - here 800 µM HOC, at an OD600 of 0.4 for 30 min. Bacteria were harvested before and after treatment in ice-cold killing buffer (50 mM Tris pH 7.5, 5 mM MgCl2, 20 mM NaN3), centrifuged at 4,750 rpm for 10 min at 4°C. The pellets were immediately frozen in liquid nitrogen and stored at -80°C. RNA isolation was performed using the acidic phenol-chloroform extraction protocol. After DNase-I treatment (Zymo Research, Germany), the RNA quality was checked by Trinean Xpose (Gentbrugge, Belgium) and the Agilent RNA Nano 6,000 kit using an Agilent 2,100 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 1,500 (San Diego, CA, United States) using 70 bp read length and a minimum sequencing depth of 10 million reads per library.

2022-12-06 | E-MTAB-11968 | 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