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Proteins of each sample were detected by 10% SDS-PAGE (Fig. 1).
Subsequently, PCR products of each sample were detected by using a 1.0%% agarose gel (Thompson et al. 2002) and purified by using a GeneJET Gel Extraction Kit (Thermo Scientific, USA).
A total of 156,516 unique splice junctions (read depth of each junction ≥ 3 in each sample) were detected using TopHat [ 15] (in Additional file 2: Table S11); 122,693 (78.4%) of them confirmed 74.1% of all known 165,564 exon-exon junctions in the B. rapa genome.
The LightCycler® 480 II analyzed the samples in 2 steps: (i) PCR amplification of the target region where the target amplicon for each sample were detected between the annealing and elongation as sigmoid curves at 640 nm (see Figure 2) (ii) Tm calling using the LightCycler 480®software to determine the melting temperature (Tm) specific for each subtype in the samples (see Figure 3).
P1 and ER1 shared 5 regions (gain of 1p22p35 and 9q31, and loss of 17p13 and depletion of whole chromosomes 12 and 16), while specific changes of each sample were detected (8p22p23 and 15q22q26 in P1; 16q24 in IR1; and 5p15, 10q22 and 22q13 in ER1).
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Each sample was detected for three repetitions.
Each sample was detected three times respectively, and the mean value of the results was taken.
The OsUbc13 protein in each sample was detected by western bolt using the anti-hUbc13 monoclonal antibody 4E11 (Andersen et al. [2005]).
Each sample was detected in duplicate repeat.
Each sample was detected in triplicate repeat.
Each sample was detected two or three times.
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