Control (CH1): 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 GA and cultured for 3 d. The concentration of the plant hormone was adjusted to 10 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 labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference. *Murashige, T. andSkoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473-497. Target (CH2): Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, GA, Callus
Normalized log2 ratio of means defined by CH2_RAW/CH1_RAW
Ratio of Means
Unnormalized ratio of means defined by CH1_RAW/CH2_RAW
CH1_RAW_spot1
Signal intensity at control spot 1 (Left side of the glass. Background-noise-processed value quantified by ArrayGauge)
CH1_RAW_spot2
Signal intensity at control spot 2 (Right side of the glass)
CH1_RAW
Mean signal intensity of control spots 1 and 2
CH2_RAW_spot1
Signal intensity at target spot 1 (Left side of the glass)
CH2_RAW_spot2
Signal intensity at target spot 2 (Right side of the glass)
CH2_RAW
Mean signal intensity of control spots 1 and 2
Flags
Has a value of 1 if any spot was determined to be unsatisfactory through PRIM filtering (Kadota, K. 2001 Physiol. Genomics, 4, 183); otherwise has a value of 0
