XR-seq of Arabidopsis csa1csa2 mutant
10 days old seedlings were exposed to 120 J/m2 UV-C. After 30-min incubation in the dark, the seedlings were frozen with liquid nitrogen, and were ground using mortar and pestle. The resulting powder was resuspended in 400 l of STES buffer (200 mM Tris?HCl pH 8.0, 500 mM NaCl, 0.1% SDS, 10 mM EDTA) and 400 l of phenol:chloroform (20:1). The sample was homogenized by vortexing with acid-washed glass beads for 30 min at 4C, followed by centrifugation at 14000 rpm for 10 min at room temperature. The supernatant was treated with 10 l of RNAseA (R4642; Sigma) for 1 hour at 37C, then with 10 l of proteinase K (P8107S; NEB) for 1 hour at 60C. 5' and 3' adapters compatible with the Illumina TruSeq Small RNA protocol were ligated to excision products. Ligation products were immunoprecipitated with CPD antibodies and the CPDs were reversed by CPD photolyase treatment. Analytical PCR was performed using one percent of the sample to decide the minimum number of cycles required for preparative scale PCR amplification. The repaired ligation products were PCR-amplified using 50- and 63-nt-long primers adding specific barcodes compatible with the Illumina TruSeq Small RNA kit. The correct size PCR products representing the library were gel purified, and then sequenced in the Illumina HiSeq 4000 platform, and single-end 50-nt reads were generated.