HOXA5 3UTR probes
Total RNA was purified from HCT116 cells using an RNeasy Mini Kit (QIAGEN, Hilden, Germany). To obtain HOXA5-enriched RNA, target-specific biotinylated DNA probes were designed for HOXA5 3'UTR-targeted antisense sequence. One microgram of total RNA was hybridized with three mixed probes, and then, RNA-DNA complexes were purified with AMPure XP beads (Beckman Coulter, Brea, CA). Purified RNA-DNA complexes were captured with Capture Beads, and they were subjected to reverse transcription and double strand-cDNA amplification with SMARTer Target RNA Capture for Illumina (Clontech, Mountain View, CA). Double strand-cDNAs were fragmented by an ultrasonic sonifier (BRANSON, Stamford, CT). The fragmented DNA was tagged and amplified with the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs, Beverly, MA). Readings encompassing HOXA5 coding sequences were measured using MiSeq (Illumina, San Diego, CA). Data were analyzed using Trimmomatic program and Integrative Genomics Viewer.