p53-inducible long non-coding RNAs encode functional peptides in hepatocellular carcinoma cells [Ribo-seq]

To globally analyse the lncRNAs with potential coding ability upon DNA damage, we performed Ribo-seq using ADR-treated HepG2 cells. The HepG2 cells were treated with 500 ng/mL ADR for 24 h, and cycloheximide (CHX) was added to inhibit the translational elongation of ribosomes.Furthermore,we identified the candidate ORFs with the selected RPF reads using the RiboCode software. Ribo-seq profiles of HepG2 p53 wild-type (WT) treated with ADR were generated by deep sequencing, in two independent experiments, using Xten Illumina sequencing platform. The ribo-seq data of the two biological replicates were integrated.Then,for the analysis of Ribo-seq data, sequenced reads that were trimmed for the adaptor sequence were aligned to the UCSC hg19 reference genome by STAR (version 2.4.2a) with parameters provided by the RiboCode (version 1.2.10) manual.