Trans-acting long non-coding RNA modulates long-range chromatin interactions associated with oncogenic MYC signaling [Iso-Seq]

To investigate the function and affected pathways of novel lncRNA IGF1R-AS1 in the prostate cancer, we established VCaP cell lines in which IGF1R-AS1 has been knocked down by siRNA. Overall design: Total RNA was extracted using Promega ReliaPrep RNA Cell system(Z6011). 3' Race was done using 5'/3' RACE Kit, 2nd Generation (Roche). One microgram of total RNA was used for reverse transcription step with olig-anchor primer 5'-GACCACGCGTATCGATGTCGACTTTTTTTTTTTTTTTTV-3' according to the manufacturer's instructions. One microliter of the RT product was used for the subsequent PCR reaction using IGF1-AS1 exon1 specific forward primer (5'-ACTATGTTTCAGCGGCTGGT-3') and the PCR anchor reverse primer in the kit(5'-GACCACGCGTATCGATGTCGAC-3'). The PCR product was cleaned using a PCR cleaning kit(Qiagen) and submitted for PacBio sequencing.