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Genotyping was performed on the basis of 211 polymorphic SNPs and was executed using the iPLEX® Gold MassARRAY Sequenom technology.
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The CL algorithms ran on a personal computer loaded with Windows XP Professional (Microsoft, Redmond, WA), and code was executed using MatLab 2009b (MathWorks, Natick, MA) in case of iAP and as a separate executable in case of CAM.
The Trinity de novo RNAseq assembly pipeline (Inchworm, Chrysalis, and Butterfly) was executed using default parameters, implementing the --REDUCE flag in Butterfly and utilizing the Jellyfish k-mer counting approach [ 30].
Optimization based on PSO and SA was executed using MATLAB software in which 30 iterations with 50 populations were used to run the program.
A multiple alignment of full-length WOX protein sequences from P. trichocarpa and P. tomentosa was executed using Clustal X2.0 [ 40], and a phylogenetic tree constructed using MEGA 4.0 by the neighbor-joining (NJ) method with 1000 bootstrap replicates.
Analysis of methylated and unmethylated CpGs was executed using two online programs: BISMA (http://biochem.jacobs-university.de/BDPC/BISMA) and QUMA (http://quma.cdb.riken.jp).jp
The analysis of moisture parameters and moisture transport was executed using a constant monitoring time domain reflectometry (TDR) method.
A 9-run design of experiments (DoE) that bracketed the range of commercially relevant mixer speeds, mixer orientations, and mass flow rates was executed using a formulation containing a cohesive drug substance at relatively low drug load.
Real Time qPCR was executed using SYBER-Green PCR Manter MiCyclerlIQd Biosystem) and an iCycleReal Real Time PCR System (Bio-Rad).
Detection of agricultural lands was executed using intra- and inter-annual Landsat images, with an overall accuracy of 86%.
The protocol was executed using three steps.
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