title: GSM3460515: DMSO_SHAPE-map; Schmidtea mediterranea; RNA-Seq
library_construction_protocol: Total RNA was extracted from worms under non-denaturing conditions as described in the manuscript. Briefly, worms were dissociated into single cells in cold calcium- and magnesium-free buffer with 1 % BSA, pelleted, treated with Proteinase K and Dnase I. Next, total RNA was extracted twice with phenol and once with chloroform. RNA buffer was exchanged to the folding buffer (100 mM HEPES, pH 8.0, 100 mM NaCl, 10 mM MgCl2). After incubation in the folding buffer at 37 C for 20 min, RNA was treated with 1M7 in DMSO or with neat  DMSO (negative control). SHAPE-MaP library construction were performed according to the amplicon workflow (Smola et al., 2015) using Nextera XT Kit (Illumina).