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For each analysis 5 biological replicates were used with two technical replicates (reverse labeling).
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The ΔΔCt relative quantification method (Livak and Schmittgen 2001), in which the expression data of the target genes were normalized with the level of expression of GAPDH (Glyceraldehyde 3-phosphate dehydrogenase) as reference gene, were used, with three technical replicates.
Eight biological replicates were used with four technical replicates.
Three biological replicates were used with three technical replicates of each.
The cDNA synthesized from six biological replicates was used to perform in RT-qPCR with two technical replications for each sample of each primer pair.
The expression analyses of co-culture samples were performed with two technical replicates using two different target cDNAs separately prepared for each sample.
Portions of the ligation products were estimated using ImageJ (http://imagej.nih.gov/ij/) densitometry analysis with two technical replicates.
Three biological replications, each with two technical replications were used for qPCR analysis.
Three biological replicates were used for each tissue sample (roots, leaves, and flowers) with two technical replicates for each biological replicate.
For each measurement, two biological replicates, each with two technical replicates were performed for both genes using the primers described above.
Data from the NimbleGen array analyzed separately using GeneSpring software (Silicon Genetics, Redwood City, CA) and represents 3 biological replicates with two technical replicates each (total n = 6).
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