<b><i>Supporting data for</i></b> "Exploring the heterogeneity of hypoxia response and investigating the role of synonymous mutations in hepatocellular carcinoma: a multi-omics analysis"

The objective of this study was to uncover the heterogeneity of the hypoxia response in hepatocellular carcinoma (HCC) and to identify functional synonymous mutations in HCC patients.<br>This dataset comprises processed data utilized in our research. The expression fold change of hypoxia-inducible genes between hypoxia and normoxia conditions was calculated using RNA-seq data. HIF1A ChIP-seq, ATAC-seq, and RRBS were performed and subsequently analyzed with MACS2 and Bismark tools. Additionally, the scRNA-seq data, derived from the 10x Genomics platform as presented by Ho D et al., was analyzed using Seurat. Synonymous nucleotide variations were identified from the whole exome sequencing (WES) data using Genome Analysis Toolkit (GATK).<br>All sequencing methodologies and data analysis adhered to standard workflows, barring instances where specific instructions were provided.