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To provide a comparison between the microarray assays and another commonly used measure of gene expression differences, qRT-PCR, gene expression differences (infected versus mock) for a set of selected genes were measured by qRT-PCR during a pilot experiment.
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Independent from p-values, agreement between the microarray assay and quantitative RT-PCR, can be seen when ordering the genes measured by qRT-PCR by their p-value: The first three genes with smallest p-values (At4g26260, At3g47340; ATable460; Table 1) are among the 4 most significant differentially expressed genes in the microarray measurements (Table 2).
The microarray assays were carried out by Takara Bio. Inc. (Otsu, Japan) using products for microarray analysis manufactured by Agilent Technologies, according to the manufacturer's protocols.
The authors thank Tomomi Fukuda, Hiroko Tadokoro, Tatsuya Suzuki, Makiko Ichikawa, Junpei Kawauchi, Satoshi Kondou, and Kamakura Techno-Science Inc. for performing the microarray assays.
EW performed the microarray assays.
CC and TW performed the microarray assays.
The Student t-test was made to explore the difference between the expression registered in the microarray assay and the qRT-PCR (Additional file 2).
In addition to Ance, the microarray assay identifies multiple genes that vary in expression level between infected and uninfected cells.
The microarray assay has recently emerged as a promising alternative for environmental pathogen monitoring.
ASAP15704 appeared to be up-regulated in the microarray assay.
Quantitative real time PCR assays were performed in order to validate the results seen on the microarray assay.
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