title: Zea mays whole seedling rep2
design: Z. mays whole seedlings were isolated in liquid nitrogen 16 days after planting. RNA was extracted from using TRIzol reagent (Life Technologies) following the manufacturer's protocol. Isolated RNA was in vitro amplified using a TargetAmp 2-round aRNA Amplification Kit 2.0 (Epicentre, catalog number TAU2R51224). Each amplified RNA sample was prepared for sequencing following the protocols of (Kumar et al. 2012) with a modified procedure for single sample processing. The libraries were ligated to barcoded adapters and pooled for 8-plex sequencing on an Illumina HiSeq 2000 at the Cornell University CLC DNA sequencing facility (http://cores.lifesciences.cornell.edu/brcinfo/?f=1).  Barcoded sequences were sorted, and then clipped. Bases with a PHRED quality score <15 were trimmed from the 3 prime end using the software package Lucy (Chou and Holmes 2001; Li and Chou 2004).