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Total RNA (from biological replicates) was extracted with RNeasy Mini kit (Qiagen), according to the manufacturer's protocol.
Total RNA from two biological replicates was extracted using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA) according to instructions.
Starch from Arabidopsis leaves (3 biological replicates) was extracted using the method described by Smith and Zeeman [ 85].
RNA for qRT-PCR analysis of the other two biological replicates was extracted by the same method, except 200 mg of ground grape tissue was used and volumes were adjusted accordingly.
Total RNA from two independent sets of plants (biological replicates) was extracted from roots, and poly-A + enriched and sRNA fractions were used to construct libraries for Illumina sequencing (see Methods for details).
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Expression values (log10) for three biological replicates were extracted using robust multi-array analysis with perfect match correction and quantile normalization.
Parallel cell culture samples (biological replicates) were extracted and reverse transcribed separately.
Consequently, a total of 30 biological replicates were extracted for each condition to minimise the biological variance in the dataset.
All stresses were pooled and three biological replicates were extracted and mixed in equal amount for cDNA synthesis.
This statistical analysis was performed using the software STATISTICA 7. Three independent biological replicates were extracted for each condition.
To validate the RNA-seq results, RNA from two additional independent biological replicates were extracted using Trizol (Invitrogen, USA) as mentioned above, and then treated with DNase I Amplification Grade (Invitrogen, USA).
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