Transcriptomics

Dataset Information

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


ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 1500, Illumina MiSeq

ORGANISM(S): Staphylococcus aureus subsp. aureus USA300  

SUBMITTER: Loi Vu Van   Haike Antelmann   Anika Winkler   Tobias Busche 

PROVIDER: E-MTAB-5666 | ArrayExpress | 2017-12-18

SECONDARY ACCESSION(S): ERP022652

REPOSITORIES: ArrayExpress, ENA

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Publications

Redox-Sensing Under Hypochlorite Stress and Infection Conditions by the Rrf2-Family Repressor HypR in Staphylococcus aureus.

Loi Vu Van VV   Busche Tobias T   Tedin Karsten K   Bernhardt Jörg J   Wollenhaupt Jan J   Huyen Nguyen Thi Thu NTT   Weise Christoph C   Kalinowski Jörn J   Wahl Markus C MC   Fulde Marcus M   Antelmann Haike H  

Antioxidants & redox signaling 20180130 7


AIMS:Staphylococcus aureus is a major human pathogen and has to cope with reactive oxygen and chlorine species (ROS, RCS) during infections, which requires efficient protection mechanisms to avoid destruction. Here, we have investigated the changes in the RNA-seq transcriptome by the strong oxidant sodium hypochlorite (NaOCl) in S. aureus USA300 to identify novel redox-sensing mechanisms that provide protection under infection conditions. RESULTS:NaOCl stress caused an oxidative stress response  ...[more]

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