The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone ABA and cultured for 3 d. The concentration of the plant hormone was adjusted to 50 microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was amplified, labeled, and hybridized 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 hormone-treated callus by the signal intensity of that from untreated callus. *Murashige, T. and Skoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473–497.
Dye-normalized signal per channel green, used for computation of log ratio
NormCH2
Dye-normalized signal per channel red, used for computation of log rati
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
1indicates Feature is a non-uniformity outlier in green channel. Flag indicating if a feature is a NonUniformity Outlier or not.
QUALITY4
1indicates Feature is a non-uniformity outlier in red channel. Flag indicating if a feature is a NonUniformity Outlier or not.
QUALITY5
1indicates 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
1indicates 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.
