title: Zea mays shoot meristem 2
design: Z. mays  shoot meristems were isolated from seedlings 16 days after planting. Meristems were fixed in ice-cold acetone overnight and processed for laser microdissection as outlined in (Scanlon et al. 2009). Approximately 100,0002  microns of cells were harvested for each biological replicate. RNA was extracted from all collected tissues with the PicoPure RNA Isolation Kit (Life Technologies, catalog number KIT0204) and 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). Trimmed reads of each species were aligned to their corresponding reference genomes using GSNAP (Wu and Nacu 2010) and uniquely-mapped reads were filtered. Uniquely mapped reads were defined as reads that aligned to the reference genome with < 2 mismatches per 36 bp, and less than 5 mismatches per 75 bp.