The japonica rice variety Nipponbare was grown under hydroponic condition for 10-days (untreated seedling sample). Seedlings were exposed to once stress conditions for 24 hours(stress treated sample). In the osmotic stress treatment, seedlings by adding 260 mM mannitol to the planter box were grown for 24 h. Total RNAs were prepared from each sample using an RNeasy Midi Kit (Qiagen, Tokyo, Japan) and the mRNAs were purified with an Oligotex-dT30 Kit (Takara, Shiga, Japan). Purified mRNA was amplified and labeled and we hybridized the 1-mg fluorescent liner amplified Cy3- and Cy5-labeled cRNAs (each cRNA was 500 ng) to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/). We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from stress-treated seedling by the signal intensity of that from untreated seedling.
Dye-normalized signal per channel green, used for computation of log ratio
NormCH2
Dye-normalized signal per channel red, used for computation of log ratio
QUALITY1
1 = Saturated or 0 = Not saturated, Flag indicating if a feature is saturated or not in green channel.
QUALITY2
1 = Saturated or 0 = Not saturated, Flag indicating if a feature is saturated or not in red channel.
QUALITY3
1 indicates Feature is a non-uniformity outlier in green channel. Flag indicating if a feature is a NonUniformity Outlier or not.
QUALITY4
1 indicates Feature is a non-uniformity outlier in red channel. Flag indicating if a feature is a NonUniformity Outlier or not.
QUALITY5
1 indicates feature is positive and significant above background in green channel. Flag indicating if the mean signal of a feature is greater than the corresponding background.
QUALITY6
1 indicates feature is positive and significant above background in red channel. Flag indicating if the mean signal of a feature is greater than the corresponding background.
