Multidimensional transcriptome dataset for systematic evaluation of Jakyakgamcho-tang-induced cell signatures

Jakyakgamcho-tang (JGT), the simplest form of herbal medicine, comprises Paeoniae Radix (PR) and Glycyrrhizae Radix et Rhizoma (GR). It has been used to treat muscle-related diseases and inflammation. However, its pharmacological effects may vary with the proportions of ingredients and preparatory factors such as the extraction method. Nevertheless, gene expression datasets systematically reflecting these variables are lacking. A total of 513 transcriptome profiles were created with three concentrations and three replicates of RNA-seq data. This dataset structure will enable multidimensional analysis of the effects of various JGT preparation factors on gene expression; these factors include the PR to GR proportional ratio (2:1, 1:1, and 1:2), solvent (water or 70% ethanol), and extraction method (combined or individual extraction method). The HepG2, C2C12, and PC12 cell lines were targeted. All raw and preprocessed data are available through GEO. Standardized metadata and ingredient data are also provided. This dataset provides a foundation for exploring traditional herbal formulations effects on cellular transcriptomic responses and can facilitate the scientific optimization of herbal medicines.