Control (CH1): The japonica rice variety Nipponbare were grown for 3 weeks at 28 degrees C under dark condition. The plants were treated with H2O for 5 hours as control plant. Whole plants used for RNA extraction. Messenger RNA was purified by Oligo(dT)-latex, labeled by Cy5, 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 RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference. Target (CH2): The japonica rice variety Nipponbare were grown for 3 weeks at 28 degrees C under dark condition. The plants were treated with 250 mM NaCl for 5 hours as target plant. Whole plants used for RNA extraction. Messenger RNA was purified by Oligo(dT)-latex, labeled by Cy5, 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 RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference. Keyword: Rice microarray project, Rice 8987 EST array, Salt, ,
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
