Analysis of Variance Components Reveals the Contribution of Sample Processing to Transcript Variation

• Type: Article in International Scientific Journal
• Date: 2009

Authors

van der Veen, D (Author) Other; Oliveira, JM (Author) Other; Van den Berg, WAM (Author) Other; de Graaff, LH (Author) Other

Journal

Title: Applied and Environmental Microbiology

Vol. 75 No. 9

Pages: 2414-2422

ISSN: 0099-2240

Publisher: American Society for Microbiology

Indexing

ISI Web of Knowledge - 20 Citations

Scopus - 23 Citations

Other information

Authenticus ID: P-00F-VRN

DOI: 10.1128/aem.02270-08

Abstract (EN): The proper design of DNA microarray experiments requires knowledge of biological and technical variation of the studied biological model. For the filamentous fungus Aspergillus niger, a fast, quantitative real-time PCR (qPCR)-based hierarchical experimental design was used to determine this variation. Analysis of variance components determined the contribution of each processing step to total variation: 68% is due to differences in day-to-day handling and processing, while the fermentor vessel, cDNA synthesis, and qPCR measurement each contributed equally to the remainder of variation. The global transcriptional response to D-xylose was analyzed using Affymetrix microarrays. Twenty-four statistically differentially expressed genes were identified. These encode enzymes required to degrade and metabolize D-xylose-containing polysaccharides, as well as complementary enzymes required to metabolize complex polymers likely present in the vicinity of D-xylose-containing substrates. These results confirm previous findings that the D-xylose signal is interpreted by the fungus as the availability of a multitude of complex polysaccharides. Measurement of a limited number of transcripts in a defined experimental setup followed by analysis of variance components is a fast and reliable method to determine biological and technical variation present in qPCR and microarray studies. This approach provides important parameters for the experimental design of batch-grown filamentous cultures and facilitates the evaluation and interpretation of microarray data.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 9