Real time PCR results for two genes. Real time PCR results confirmed correlation between position and intensity of probes afteramplification. (A-C) Data for LOC Os06g07140.1. (A) The intensity of LOC Os06g07140.1 decreased dramatically in Two-Cycle cRNA sample (TCS) comparing with One-Cycle cRNA sample (ONS) in our microarray experiment. (B) Schematic diagram of LOC Os06g07140.1. Yellow line, cDNA of the gene; Big orange arrow, coding sequence (CDS) of the gene; Green line section (A1-A6), designed amplicons in Real Time PCR experiments; Numbers in the brackets were the starting point of amplicons from 5’ end; Blue narrow arrow, designed probes on the microarray. Their starting points (unlabeled in the figure) were 421, 498, 502, 514, 547, 580, 678, 680, 684, 688, and 691. (C) Degradation Proportion (DP, see details in Methods section) of amplicons (A1-A6) showed in (B). DP decreased along with distance from the 5’ end and increased when it was too close to 3’ end because of degradation and random effect. (D-F) Data for LOC Os01g43520.1. (D) The intensity of LOCOs01g43520.1. (E) Schematic diagram of LOCOs01g43520.1. (A1-A7) were designed amplicons. The probes’ starting points on microarray were 2485, 2505, 2515, 2537, 2568, 2579, 2599, 2627, 2642, 2658, and 2669. (F) DP of amplicons (A1-A7) showed in (E). Because there was no amplicon too close to 3’ end, DP didnt increase again.