Small RNAs were sequenced using a Solexa GA. Three different linkers were used for different samples and mixed prior to sequencing. Raw data was filtered to identify small RNAs associated with each linker. Subsequently, small RNAs were filtered to remove rRNA fragments. The remainder were mapped to the Physcomitrella patens draft genome version 1.2 (using oligomap) and filtered to retain only those with one or more perfect match. This platform is all small RNA sequences from 10 day old dcl3 samples (line 5 and 10). See Cho et al. for details.
