title: Physcomitrella whole plant rep2
design: Physcomitrella patens whole plant cultures (protonemata and gametophores) were isolated in liquid nitrogen 21 days after subculture on BCD plates. 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).