Gene expression profiles of 35 paired HCC and non-tumor tissues by RNA-seq data

This study aims to uncover the transcriptomic variations in HCC Overall design: RNA-seq reads per sample were mapped to the reference using Tophat v2.0.12. The reference consists of the human reference genome and the Ensembl annotated human transcriptome (GRCh37/hg19 assembly). The overall mapping rate per sample was 92% on average. Next, the mapped reads were processed using cufflinks v2.2.1 with the 'classic-fpkm' library normalization method and 'fr-unstranded' library type to quantitate gene expression against Ensembl transcript annotation.