characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2017-09-08T17:01:26Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-08-29T14:40:18Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA104229122
characteristics.characteristic: External Id
characteristics.text: Technologieplattform Genomik, Centrum fur Biotechnologie (CeBiTec), Universitat Bielefeld, Universitatsstr. 27, Bielefeld, Germany.
characteristics.characteristic: INSDC center name
characteristics.text: 2017-09-08T17:01:26Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-08-29T14:40:18Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1888140
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-6012:CWB_Styrol_E
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: Protocols: A pre-culture of G. rubripertincta CWB2 was grown at 30 °C in minimal media with fructose and styrene as sole source of carbon, respectively. After 5 days of cultivation the culture was diluted 1/10 in fresh media and incubated for 24 h with the respective substrate in a set of four Erlenmeyer flasks. Prior harvesting the cells, 10 % of an ice-cold STOP-solution (10 % buffered phenol in ethanol) was added to the culture followed by centrifugation at 11,000 x g for 5 minutes at 4 °C. The supernatant was discarded and the pellet was stored until RNA isolation at -80 °C. A pre-culture of G. rubripertincta CWB2 was grown at 30 °C in minimal media with fructose and styrene as sole source of carbon, respectively. After 5 days of cultivation the culture was diluted 1/10 in fresh media and incubated for 24 h with the respective substrate in a set of four Erlenmeyer flasks. To break up the cells, 150 µl of a 5 mg ml-1 lysozyme solution were added to the pellet, mixed and incubated at room temperature for 5 minutes. 450 µl of buffer RLT (Qiagen) and 50 mg of (0.1 mm) glass beads were added to resuspend and break the cells by repeated vortexing at 4 °C. The suspension was applied to QIAshredder column for homogenization and to remove particles from the sample. Extraction of total RNA Extraction was done by applying the RNeasy Mini Kit including on-column DNA digestion (Qiagen). Isolated RNA was stored at -80 °C and quality was controlled on the 2100 Bioanalyzer using the RNA 6000 Nano Kit (Agilent). RNA quality and quantity was again checked by an Agilent 2100 Bioanalyzer run (Agilent Technologies, Böblingen, Germany) and Trinean Xpose sytem (Gentbrugge, Belgium) prior and after rRNA depletion by Ribo-Zero rRNA Removal Kit (Bacteria) (Illumina, San Diego, CA, USA). TruSeq Stranded mRNA Library Prep Kit from (Illumina, (San Diego, CA, USA) was used to prepare the cDNA libraries to analyze the whole transcriptome.
characteristics.characteristic: description
characteristics.text: styrene as sole source of carbon
characteristics.characteristic: growth condition
characteristics.text: Gordonia rubripertincta
characteristics.characteristic: organism
characteristics.text: Gordonia rubripertincta
characteristics.characteristic: organism
characteristics.text: Gordonia rubripertincta
characteristics.characteristic: scientific_name
characteristics.text: CWB2
characteristics.characteristic: strain
characteristics.text: CWB_Styrol_E
characteristics.characteristic: title