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

• Tipo: Artigo em Revista Científica Internacional
• Data: 2009

Autores

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

Revista

Título: Applied and Environmental Microbiology

Vol. 75 Nº 9

Páginas: 2414-2422

ISSN: 0099-2240

Editora: American Society for Microbiology

Indexação

ISI Web of Knowledge - 20 Citações

Scopus - 23 Citações

Outras Informações

ID Authenticus: 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.

Idioma: Inglês

Tipo (Avaliação Docente): Científica

Nº de páginas: 9