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A pipeline for functional characterization of ncRNAs in plants. SHAPE, RNA-selective 2′-hydroxyl acylation and primer extension; PARS, parallel analysis of RNA structure; DMS-seq, dimethyl sulfate-modified RNA for sequencing; CHIRP, chromatin isolation by RNA purification; CHART, capture hybridization analysis of RNA targets, CLASH, crosslinking, ligation, sequencing of hybrids; CLIP, crosslinking immunoprecipitation.
