It has been demonstrated that antisense RNA amplification not only preserves the fidelity of RNA-based microarray analysis but even improves the sensitivity.
This indicates the need of robust noise models, which can handle outlying data points well and suggests that Gaussian noise models are unsuitable for microarray data analysis, even if according to Novak et al. (2006) only about 5 15% of samples are non-Gaussian distributed.
Microarray analysis showed that even without H2O2 challenge, some genes involved in oxidative damage protection were up-regulated, presumably in response to an increased level of internal H2O2, due to deletion of the SO1377 gene.
Although three rounds of amplification yielded enough quantity of RNA for microarray analysis (>20 μg) even in the case of 2 pg RNA, scatter plot analysis revealed that the qualities of the obtained results were quite different between the samples from 5 μg and 2 pg RNA.
A striking finding of our microarray analysis is that Bergmann glia, even in the adult, express numerous genes thought to be expressed specifically by stem cells (Table 8), and show enrichment of the embryonic stem cell pluripotency pathway (Table 6).
Interestingly, a promoter, designated as chr7_-_74867620 (unannotated promoter), was affected in opposite ways (see Supplementary Table S2 online), even though microarray analysis did not detect significant expression changes at our working drug dosage.
Perhaps because of the stringency with which we performed both the microarray analysis and the experimental validation, even here the small changes predicted by microarray were consistently seen with the qRT-PCR data, although the quantitative correlation was not as strong overall as for data showing larger changes.
Analysis of EST frequency comprising a contig and the source of the contig provides an insight with respect to the spatial expression level and biochemical functions even without subsequent microarray analysis.
The drastically different structure of these high-sensitivity transcriptome profiles requires adaptation or even redevelopment of the standard microarray analysis methods.
One gene, plg, had no expression change in control versus treated embryos, even though it was identified through microarray analysis to be affected by As3+.
