design: Pull-downs were performed with 15 g RNA, 8.7 nmol DTB-preQ1 (4b) ligand and 20 L M-280 Streptavidin Dynabeads. After the final washing step, the beads were resuspended in 10 L RNAse-free water. Next, a library was prepared using the "Short Insert Sizes" protocol of the CORALL RNA-Seq V2 Library Prep (Lexogen). Since initially the RNA was still bound to the beads, the Displacement Stop Primer hybridization and reverse transcription were performed on the beads. Then, the beads were discarded and the supernatant was used for the subsequent steps according to the manufacturer's instructions.