Real-time PCR quantification failed to amplify ESTs C06013D07 and IC0AAA56DH07 that exhibited, respectively, microarray hybridization signal ratios of 0.23 and 0.30 in ITA, indicating that microarray data of these two ESTs was most likely affected by nonspecific cross-hybridization.
Microarray hybridization experiments indicated M. grisea genes expressed during nitrogen limitation were also expressed during in planta growth [ 13, 14].
However, PCR and DNA microarray hybridization experiments indicated that this plasmid was absent in other clone SA isolates (data not shown), suggesting that pVir, although present in IA3902, is not required for abortion induction.
High SFP detection performances of both genome and transcript hybridizations indicated that microarrays of a complex genome (e.g., of Oryza sativa) can be effectively utilized for whole genome genotyping to conduct mutant mapping and analysis of quantitative traits such as gene expression levels.
For the mutant strain, both microarray hybridization and qRT-PCR indicated that so2426 expression levels were not detectable above background, thus providing additional confirmation of deletion of the so2426 gene.
Among them, 46 (81%) genes exhibited expression patterns consistent with the microarray results (t-test, p < 0.01, see Additional file 3), indicating that our microarray hybridization results indeed reflect the relative in vivo expression level of each gene.
Our results clearly indicate that the microarray hybridization presented in this study represents a very robust method to screen whole sets of P. aeruginosa strains bearing unknown genetic variations.
Quantitative RT-PCR analysis for 31 selected genes indicated high conformity to results from the microarray hybridization.
Recent experiments indicate that the underlying principles governing DNA microarray hybridization – and in particular MM discrimination – are not completely understood.
Microarray hybridization and washing were performed using reagents and instruments (hybridization chambers and rotating oven) as indicated by the manufacturer (Agilent Technologies).
