characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-06-06T15:00:05Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-06-06T15:00:05Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA112203290
characteristics.characteristic: External Id
characteristics.text: Philipps-Universitat Marburg Center for Synthetic Microbiology (Synmikro) Becker lab
characteristics.characteristic: INSDC center name
characteristics.text: 2023-06-06T15:00:05Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-06-06T15:00:05Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS14314233
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12482:delta ramB ac R2
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: Protocols: Samples for transcriptome analysis were taken in triplicates from succinate- and acetate-growing cultures of P. denitrificans Pd1222 and the Pd1222 ΔramB mutant. Strains were grown in mineral salt medium supplemented with trace elements TE3-Zn (Hahnke et al. 2014, DOI: 10.3389/fmicb.2014.00018 ) and defined carbon compounds to a total carbon concentration of 120 mM at 30°C. At OD600=0.8, cells were collected by centrifugation at 10,000 x g and 4 °C for 10 min. After removal of supernatant, cell pellets were snap-frozen in liquid nitrogen and stored at -80 °C until further usage. The Qiagen miRNeasy Kit was used for total RNA isolation starting from a pellet of 4 mL cultured cells. The pellet was resuspended in 1 mL QiAzol lysis reagent and homogenized in a FastPrep sample preparation system using Lysing Matrix B containing 0.1 mm silica beads (MP biomedicals) and the following settings: 4x 6,500 rpm for 20 sec, 15 sec break. The supernatant was transferred into a new tube and RNA isolation was performed according to the manufacturer’s instruction including the optional on column DNaseI digestion. Depletion of rRNA was performed and cDNA libraries were prepared with the Illumina® Stranded Total RNA Prep Kit (Ligation with Ribo-Zero Plus) according to the manufacturer’s instructions.
characteristics.characteristic: description
characteristics.text: vegetative growth
characteristics.characteristic: developmental stage
characteristics.text: delta ramB
characteristics.characteristic: genotype
characteristics.text: acetate
characteristics.characteristic: growth condition
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Paracoccus denitrificans PD1222
characteristics.characteristic: organism
characteristics.text: Paracoccus denitrificans PD1222
characteristics.characteristic: organism
characteristics.text: whole organism
characteristics.characteristic: organism part
characteristics.text: Paracoccus denitrificans PD1222
characteristics.characteristic: scientific_name
characteristics.text: delta ramB ac R2
characteristics.characteristic: title