Marchantia whole plant rep2
Marchantia polymorpha whole plants were isolated in liquid nitrogen 9 days after plating gemmae. RNA was extracted 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).