Comparison of expression levels in our microarray assays indicates that Fd-GOGAT1 (GLU1; At5g04140) is more highly expressed in leaves than in roots (signal intensity: log2 = 10.84 versus log2 = 5.06; Δlog2 = 5.78) of 18 day old in vitro grown A. thaliana wild type plants (Col-0 ecotype) (Additional file 1).
The result for galp was likely a false positive from the microarray, in which the more sensitive real-time PCR assay indicated no statistical differential expression of this gene.
Microarray assays have indicated that the gene expression profile was altered in the liver of SCD knockout mice, and the most obvious pattern was down-regulation of the genes involved in lipogenesis and up-regulation of the genes associated with fatty acid β-oxidation [ 8].
Our microarray data showed that DKK1 was up-regulated in PTTG1−/− cells and the further in vitro assays indicated that DKK1 was down-regulated by over expressing either FoxM1 or PTTG1.
Each figure shows the microarray data (A) confirmation of gene expression by qPCR (B) and the ChIP data (C) with the position of the ChIP qPCR assays indicated below.
Beta-galactosidase activity assays indicated that the expression of these two genes was induced under iron limitation and derepressed in the fur mutant strain, validating the microarray data.
ERK regulates the latent process in a transcription-dependent manner, as indicated by the microarray assay (see Table S1), whereas ERK regulates the extension process in a transcription-independent manner (Figure 5A), indicating context-dependent, diverse functions of ERK for cell differentiation.
However, detection of this mRNA on the microarray scan and its subsequent verification by RT-PCR analysis indicates the sensitivity of the microarray assay.
We found that eighteen TFs changed less than 2-fold in the microarray assay, but changed over 5 times in the qRT-PCR analysis, indicating that qRT-PCR is much more sensitive than the Genechip assay.
The genomic microarray assay involves three steps with three levels of capture-target-intermediate oligo hybridization as indicated in Fig. 1.
