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We measure the intensity drained by the device at different phases by using the default software.
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Box plots were generated using the default R software options.
Libraries were sequenced on either an Illumina GAIIx or an Illumina HiSeq using the default RTA analysis software.
Removal of the rRNA sequences from the dataset was done using two iterative steps, first by applying the SortMeRNA software using the default rRNA database included in the software package, which consist of 16S, 23S, 18S, and 28S rRNAs [ 53].
The peak shift Δδ was set by using the default parameters of the software package and signal-to-noise ratio (S/N) was set to 100.
Detection calls (Present, Absent and Marginal) were determined using the default parameters of the software.
The genes and experiments were median centered and normalized using the default method for this software.
The analyses were performed by using the default setting in both software with a significance threshold p-value < 0.05.
The alignments were screened using the default parameters of RNAcode (software available at http://wash.github.com/rnacode) and a p-value cutoff of 0.05.
Primers were designed for coding sequences of the candidate reference genes from the Prunus persica genome, available at the Genome Database for Rosaceae (GDR, − http://www.rosaceae.org/), using the default parameters of the software Primer3Plus [ 57].
The threshold and threshold cycle values were automatically determined by the Rotor Gene 6.0.19 software, using the default parameters.
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