TREseq analysis in Arabidopsis T87 cultured cell (pair-end sequencing)

In a previous study, a high-throughput approach for genome-wide profiling of RNA cleavage sites was developed (e.g. Parallel analysis of RNA end (PARE), 5'P sequencing (5Pseq), Genome-wide mapping of uncapped transcripts (GMUCT)), However, there were some problems with experimental procedures (e.g. Many of the cleavage sites may be mapped in the 3' transcripts; It was difficult to accurately identify the multiple cleavage sites in one mRNA). Thus, we performed truncated RNA end sequencing (TREseq) using 3 day after inoculation of Arabidopsis T87 cultured cell to determine the truncated 5' RNA ends (cleavage sites). In this analysis, we conducted TREseq analysis by pair-end sequencing to improve read information. In addition, we conducted TREseq without Cap-trapping method to check the concentration of Cap and Cap-less RNA.