title: mRNA-seq of Arabidopsis rosette: RRGD Timepoint IX - recovery 60 min + repeat excess-light 60 min rep  2
design: RNA was isolated using Trizol Reagent (Life Technologies Australia Pty Ltd) using a procedure adapted from Allen et al. (2010). RNA-seq libraries were prepared using the Illumina TruSeq V2 kit (RS-122-2001) as per the manufactureres instructions (TruSeq User Guide Revision D). Four micrograms of total RNA was used for input and fragmented for 7 minutes. Using pilot PCRs, an optimal PCR cycle number of 10 cycles was determined empirically for amplification of all samples and final amplification was performed with a half volume PCR.  Following PCR clean-up samples were pooled in equal molar ratios and sequenced over 2 lanes on the HiSeq2000 in 100bp paired-end mode.