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.

本研究旨在揭示肝细胞癌（HCC）缺氧反应的异质性，并识别HCC患者中的功能性同义突变。本数据集包含了我们研究中使用的处理后的数据。通过RNA测序数据计算了缺氧与常氧条件下缺氧诱导基因的表达倍数变化。进行了HIF1A ChIP-seq、ATAC-seq和RRBS实验，并使用MACS2和Bismark工具进行了后续分析。此外，分析了来自10x Genomics平台的单细胞RNA测序（scRNA-seq）数据，采用Seurat进行。通过全外显子测序（WES）数据，使用基因组分析工具包（GATK）识别了同义核苷酸变异。所有测序方法和数据分析均遵循标准工作流程，除非有特定指令。