Illumina HiSeq 1500 paired end sequencing; RNA-seq system comparison of Streptomyces lividans TK24 cultivated under micro-scale biolector and reference bioreactor conditions
RNA-seq system comparison of Streptomyces lividans TK24 cultivated under micro-scale biolector and reference bioreactor conditions
S. lividans TK24 grown in a 1.5 L lab-scale system (DasGip, Jülich, Germany), equipped with two six blade, 46 mm Rushton turbines as well as sensors for DO (Hamilton, Visiferm DO 225) and pH (Mettler–Toledo, 405-DPAS-SC-K8S/225/120). in modified minimal medium NMMP (D'Huys et al. 2011) was applied, containing 2.07 g/L NaH2PO4 x 1 H2O, 2.6 g/L K2HPO4, 0.6 MgSO4 x 7 H2O, 3.0 g/L (NH4)2SO4, 10 g/L D-glucose and 5 g/L BactoTM Casamino acids as well as several trace elements (1 mg/L ZnSO4 x 7 H2O, 1 mg/L FeSO4 x 7 H2O, 1 mg/L MnCl2 x 4 H2O, 1 mg/L CaCl2), harvested in late growth phase. Temperature was controlled at 30 °C. Both, aeration and agitation were set to fixed values at 0.5 vvm and 800 rpm respectively. Briefly, S. lividans TK24 cells were harvested at late growth phase. Total RNA was isolated from two biological replicates using RNeasy Mini Kit along with a DNase Kit (both from Qiagen). Initially RNA quality was checked by Trinean Xpose (Gentbrugge,Belgium) and Agilent RNA Nano 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). Samples contaminated with DNA were treated with DNase (Qiagen), cleaned as described above and rechecked by Xpose and Agilent Bioanalyzer.  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, Böblingen, Germany).
Experimental Factor: Bioreactor 1.5 L lab-scale system (DasGip)
growth condition