Supporting data for "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.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).All sequencing methodologies and data analysis adhered to standard workflows, barring instances where specific instructions were provided.