Determination of variability of fermentor-grown Aspergillus niger

Knowledge of the biological and technical variation for fermentor-grown Aspergillus niger cultures is needed to design DNA microarray experiments properly. We cultured A. niger in batch-operated fermentor vessels and induced with D-xylose. Transcript profiles were followed in detail by qPCR for 8 genes. A variance components analysis was performed on these data to determine the origin and magnitude of variation within each process step for this experiment. 6 Fermentor cultures were selected to determine technical and biological variation for all 14554 ORFs present on this array type. Keywords: Validation of microarrays; variation analysis; experimental design For 5 weeks, 4 batch-fermentation per week were run in which A. niger was grown on 100 mM sorbitol. At 14 hours after oxygen supply had switched from headspace to sparger-inlet each fermentor was induced with either 0.1 mM D-xylose or 0.1 mM sorbitol. Samples were harvested just before induction and 1 hour after induction. Per week, 3 fermentors were induced with D-xylose and 1 fermentor was induced with sorbitol. Six samples were selected to be put on microarrays based on their biomass density, time distribution, magnitude of xylose-induced genes as measured by qPCR, fermentor vessel number.