LHD participated in designing the experiments, carried out irradiation, microarray assays, data analysis and quantitative RT-PCR.
CH conducted experimental design, supervised microarray assays, conducted data interpretation, and contributed to the manuscript.
KFL and YFW made the most important contributions to the manuscript, they performed most part of this study, including samples preparation, microarray assays and data analysis, and also writing the manuscript.
The complete data sets of this study including both microarray and TaqMan® assay data can be accessed from GEO with accession number GSE9106.
MP performed all Western blots, ELISAs and immunohistochemistry. DS carried out cell culture experiments and JLE performed DNA microarray assay and corresponding data analysis.
The lack of amplification of Os11g02330 and Os04g033930 was inconsistent with the microarray and GUS assay data (Figs 3 and 4).
For example, highly expressed RPN4 in this study was found to be regulated by Yap1p, Pdr1p, Pdr3p, and Hsf1p that supported by ChIP-chip data and microarray assay of transcription factor mutations [ 32- 37].
Hence, as for the microarray assays, we analyzed data from a total of 18 replicates at least (3 biological replicates × 3 within plate technical replicates × 2 technical replicates i.e. repeated measurements) obtained from each real time PCR experiment.
Even though the average fold changes for most of these signature genes are relatively small (mostly<2-fold), these were reproducible, as shown by 89% concordance between the TaqMan assay data and the microarray data (Table S4).
