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At the end of each "paired" extended basic CCE, the expert graded the global imaging quality of his examination as: "high quality," "moderate quality" or "low quality".
For the interaction studies, protoplasts (100 μl) (1.5-2 × 106 cells) were transformed with 2.5-5 μg of each paired construct (Vn-OsRap2.6 + RACK1A-Vc), (Vn-OsRap2.6 + Vc-OsMAPK3/6) and a negative control (Vn-OsRap2.6 + GUS-Vc) by the polyethylene glycol (PEG) method with minor modifications (Yoo et al 2007).
PCR amplification of the cDNA was performed in a reaction mixture with a final volume of 30 µL containing 2 µL of 4×dNTPs, one unit of Taq DNA polymerase, and 10 mmol/L of each paired primer specific to EPR-1 and Survivin, respectively.
The total length of each paired end sequencing run was 200 cycles.
The PEMQsta program reads the MQV pairs, computes the minimal value of each paired MQVs as the PE-MQV, and generates the distribution of PE-MQV.
Next, the reads of each paired window were combined and then re-sampled based on the initial ratio of that window's number of reads.
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