KORE-Map 1.1: Korean medicine omics resource extension map on transcriptome data of dyspepsia herbal medicine

Herbal medicines have been used for centuries to manage various disease; however, their therapeutic mechanisms remain complex and insufficiently understood. Unlike standardized pharmaceuticals, prescriptions may vary among patients with similar conditions, reflecting the individualized principles of traditional medicine. To systematically explore these mechanisms, we generated a drug-induced transcriptome dataset focused on herbal medicines prescribed for dyspepsia. We aimed to create a reusable, high-quality resource that enables comparative analyses across cell types, solvents, and concentrations. KORE-Map 1.1 generated 1,075 bulk RNA-seq profiles from four human cell lines (A549, HepG2, HT29, and SW1783) treated with four dyspepsia prescriptions and their constituent herbs. Extracts were prepared in hot water and 70% ethanol and applied at three concentrations. RNA integrity, sequencing quality, and reproducibility were validated, with a median mapping rate of 96.19% and strong biological and technical correlations across replicates and batches. Compared with Connectivity Map, the drug-induced signatures showed consistent patterns at the pathway level. All datasets were deposited in GEO under accessions GSE252820, GSE248976, GSE250627, and GSE254458. This resource provides a foundation for studies in herbal pharmacology, systems biology, drug discovery, and mechanism-based repurposing.