Analysis of variance components reveals the contribution of sample processing to transcript variation.

ABSTRACT: 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 a

SUBMITTER: van der Veen D 

PROVIDER: S-EPMC2675206 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature