Parallel analysis of RNA ends (PARE)

PARE libraries were prepared as previously described [36, 124] at the Donald Danforth Plant Science Center in St. Louis, MO and sequenced on a HiSeq 2500 (Illumina, Inc.) at the University of Delaware. Reads were quality assessed using the FastQC program version 0.11.3 [113]. Reads were quality filtered and adapters were trimmed using Trimmomatic version 0.33 [114]. The two PARE analysis programs sPARTA (version 1.21) [31] and CleaveLand (version 4.4) [32] were used independently to identify likely sRNA targets using sRNA sequencing data, the barley transcriptome (ensembl version 38) [53], and PARE sequencing data. PARE validated targets were filtered based on adjusted p-values using a 1% false discovery rate along with a PARE category of less than 2 (with sPARTA data).