The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments in HuH-7 cells

To globally analyse the lncRNAs with potential coding ability of HCC cells, we performed Ribo-seq using HuH-7 cells. The cycloheximide (CHX) was added to inhibit the translational elongation of ribosomes of the HuH-7 cells.Furthermore,we identified the candidate ORFs with the selected RPF reads using the RiboCode software. Ribo-seq profiles of HuH-7 cells 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.