Data for the article "Single-cell eQTL analysis identifies genetic variation underlying metabolic dysfunction-associated steatohepatitis"

This dataset contains data associated with the following article: Hong, S.E., Mun, S.J., Lee, Y.J. et al. Single-cell eQTL analysis identifies genetic variation underlying metabolic dysfunction-associated steatohepatitis. Nat Genet (2025). https://doi.org/10.1038/s41588-025-02237-8 This dataset includes following: Gene expression matrices per sample obtained from cellranger output Processed snRNA-seq data with cell-level and sample-level metadata in Seurat v4 format hdWGCNA results including harmonized module expression (hME) values for each single cell and module information Expression and covariate matrices used for sc-eQTL analysis Full summary statistics (including non-significant pairs) of sc-eQTLs (liver-eQTL, MASLD-eQTL, and control-eQTL) A table of significant liver-eQTLs and ieQTLs with comprehensive annotations A list of GWAS-colocalizing liver-eQTLs A list of 601 quartets composed of ieGenes, ieSNPs, interacting cell states, and transcription factors (TFs) Bulk RNA-seq data newly generated during revision Bulk RNA-seq counts matrix and differentially expressed gene list from hepatic organoids treated with EFHD1 siRNA Bulk RNA-seq counts matrix and differentially expressed gene list from hepatic organoids treated with FOXO1-specific inhibitor AS1842856 Bulk RNA-seq counts matrix and differentially expressed gene list from HeG2 treated with FOXO1-specific inhibitor AS1842856本数据集关联以下研究论文： Hong, S.E., Mun, S.J., Lee, Y.J. 等. 单细胞表达数量性状位点（single-cell eQTL, sc-eQTL）分析揭示代谢功能障碍相关脂肪性肝炎的遗传调控基础. 《自然·遗传学》（Nat Genet）(2025). https://doi.org/10.1038/s41588-025-02237-8 本数据集包含以下内容： 1. 由Cell Ranger输出得到的单样本基因表达矩阵 2. 采用Seurat v4格式存储的预处理单细胞核RNA测序（single-nucleus RNA sequencing, snRNA-seq）数据，包含细胞水平与样本水平的元数据 3. 高维加权基因共表达网络分析（high-dimensional weighted gene co-expression network analysis, hdWGCNA）结果，涵盖每个单细胞的协调模块表达（harmonized module expression, hME）值及模块相关信息 4. 用于sc-eQTL分析的表达矩阵与协变量矩阵 5. 三类sc-eQTL（肝脏eQTL、代谢功能障碍相关脂肪性肝炎eQTL、对照eQTL）的完整汇总统计数据（包含非显著位点对） 6. 一张包含全面注释的显著肝脏eQTL及交互表达数量性状位点（interaction expression quantitative trait loci, ieQTL）表格 7. 与全基因组关联研究（genome-wide association study, GWAS）共定位的肝脏eQTL列表 8. 由交互基因（interaction gene, ieGene）、交互位点（interaction SNP, ieSNP）、交互细胞状态及转录因子（transcription factor, TF）组成的601个四重组列表 9. 论文修订阶段新生成的批量RNA测序（bulk RNA-seq）数据： - 经EFHD1小干扰RNA（small interfering RNA, siRNA）处理的肝类器官的批量RNA测序计数矩阵与差异表达基因列表 - 经FOXO1特异性抑制剂AS1842856处理的肝类器官的批量RNA测序计数矩阵与差异表达基因列表 - 经FOXO1特异性抑制剂AS1842856处理的HeG2细胞的批量RNA测序计数矩阵与差异表达基因列表