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The miRNA count was normalized (RPKM), and the fold change was obtained for each miRNA comparison.

Normalized counts of unigenes for calculating gene fold changes were obtained from the multi-condition analysis.

Fold changes were obtained by using the formula 2∧- ΔΔct).

Fold changes were obtained by comparing expression level to that under normal growth conditions (Sample A).

The fold changes were obtained using linear RQ values.

The fold changes were obtained using the ∆∆Ct method [ 51].

Quantitative fold changes were obtained using the comparative threshold cycle (ΔΔCT) method, as recommended by Applied Biosystems.

At all time points, fold changes in gene expression levels were obtained for each oncogene compared to empty vector control as described in Materials and Methods.

At least three-fold redundancy was obtained for each segment.

Highest fold-change expression levels were obtained for contigs representing various members of the sporamin and β-amylase genes, exhibiting 174- to 1,467-fold 1,467-foldexpression.

Fold changes of around 1 were obtained for At1g08530-like and MDP0000934866 (At1g06150-like) for all tissues with the exception of a 2.5-fold induction of MDP0000934866 in one of the shoot apical meristem samples.