Transcriptome Analysis of Chemostat and Retentostat Yeast Cultures

RNA was isolated from cell pellets from chemostat and retentostat cultivations using the Tri reagent according to the supplier's instructions (Ambion, USA). Cells were disrupted by glass beads using a ribolyser (MP Biomedicals). To remove residual DNA, the RNA samples were treated with the DNA-free™-kit (Ambion) according to the manufacturer’s manual. Subsequently, RNA quality, purity, and concentration were analyzed by a NanoDrop™ spectrophotometer and Bioanalyzer (Agilent). For cDNA synthesis for qPCR, the Biozym cDNA synthesis kit (Biozym) in combination with oligo(dt)₂₃ primers (NEB) was used. Quantitative PCR was carried out using the Biozym Blue Probe qPCR kit on a Rotor Gene Q instrument (Qiagen). Changes in transcript levels were calculated relative to the reference sample after normalization to ACT1 (PP7435_Chr3-0993) expression using the threshold cycle method of the Rotor Gene software. A more detailed description and a list of the used primers is provided in Additional file 1.