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

ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 1500

ORGANISM(S): Streptococcus pneumoniae D39

SUBMITTER: Tobias Busche 

PROVIDER: E-MTAB-11968 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress