Identification of DAMER-interacting RNAs by RNA-RNA pulldown assay and sequencing [RNA-Seq]

This experiment aimed to identify all transcripts that directly interact with the lncRNA DAMER. Full-length DAMER was transcribed in vitro and biotinylated at the 3' end. The biotinylated DAMER was used as a probe to capture interacting RNAs from 95D cell lysates. The captured RNAs were then eluted and subjected to high-throughput sequencing to identify transcripts specifically enriched by DAMER. Overall design: 95D cells were cultured under nutrient deprivation for 48 hours to induce the relevant cellular state. Full-length DAMER was transcribed in vitro and biotinylated at the 3' end. The biotinylated DAMER was used as a probe to capture interacting RNAs from 95D cell lysates. The captured RNAs were then eluted and subjected to high-throughput sequencing.