characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-01-09T00:14:28Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-01-09T00:14:28Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA112245953
characteristics.characteristic: External Id
characteristics.text: Omics Core Facility NGS Unit Medical School OWL & CeBiTec Bielefeld University
characteristics.characteristic: INSDC center name
characteristics.text: 2023-01-09T00:14:28Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-01-09T00:14:28Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS14356827
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12470:P_putida_wt_3_1_mM_octanol
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: Protocols: Here, we explored membrane adaptations of Pseudomonas putida KT2440, in particular outer membrane vesicle (OMV) formation in response to 1-octanol, PQS and prodigiosin, causing chemical membrane stress via RNA-seq of mRNA. Pseudomonas putida wild type KT2440 (Nelson et al. 2002) and the derived strains P. putida pig21 were cultivated in biological triplicates under continuous shaking (130 rpm) at 30 °C in 10 mL LB (lysogeny broth) medium (10 g L-1 tryptone, 5 g L-1 yeast extract, 10 g L-1 sodium chloride; Carl Roth®, Karlsruhe, Germany). Antibiotics were added to the culture medium when appropriate to the following final concentrations: 25 µg mL-1 kanamycin, 25 µg mL-1 irgasan, 25 µg mL-1 gentamicin, 50 µg mL-1 tetracycline. For chemical induction of OMV formation, P. putida KT2440 was exposed to 1 mM 1-octanol or 50 µM PQS (Pseudomonas quinolone signal) after reaching the logarithmic growth phase. Cell pellet was harvested after 7 h, adjusted to an optical density (OD700 nm) of 1 by centirfugation and flash frozen in liquid nitrogen. Total RNA was isolated from 3 biological replicates using Quick-RNA Miniprep Plus kit (Zymo Research). The samples were treated with DNase (Zymo Research) and RNA was again purified with an RNA Clean&Concentrator-5 kit (Zymo Research). Ribosomal rRNA was removed with a riboPOOL for bacteria (siTOOLs Biotech GmbH). The purity of RNA and removal of rRNA was then tested with an Agilent RNA Pico 6000 kit and an Agilent 2100 Bioanalyzer (Agilent Technologies). After ribosomal rRNA was removed with a riboPOOL for bacteria (siTOOLs Biotech GmbH), Illumina TruSeq Stranded mRNA Sample Preparation guide was then used to construct the cDNA library.
characteristics.characteristic: description
characteristics.text: wild type genotype
characteristics.characteristic: genotype
characteristics.text: LB broth
characteristics.characteristic: growth condition
characteristics.text: Pseudomonas putida KT2440
characteristics.characteristic: organism
characteristics.text: Pseudomonas putida KT2440
characteristics.characteristic: organism
characteristics.text: whole organism
characteristics.characteristic: organism part
characteristics.text: Pseudomonas putida KT2440
characteristics.characteristic: scientific_name
characteristics.text: KT2440
characteristics.characteristic: strain
characteristics.text: P_putida_wt_3_1_mM_octanol
characteristics.characteristic: title