Supporting data for "Modelling the drug response of on patient-derived organoids to identify combinatorial therapies for diffuse-type gastric cancer"

The study used patient-derived organoids (PDOs) established from patients with gastric cancer to perform drug response characterization and combinatorial drug screens, aiming to dissect drug mechanism, and enhance treatment efficacy by identification of combinatorial drug partners.

For data sourced from previous literature and available publicly, the raw datafiles are included for reference.

For drug response characterization, drug mechanism was dissected through comprehensive analysis of gene expression changes at both bulk and single cell levels. Bulk RNAseq and single cell RNAseq were performed in parallel, with 3 treatment conditions on 8 PDOs. The dataset files include the Log2TPM value of the 24 bulk RNAseq samples, and the count matrix for each of the 24 single cell RNAseq samples.

For combinatorial drug screening, the combinatorial synergy was evaluated for 24 drug combinations. For 10 of these combinations, the combinatorial synergy was evaluated on 15 PDOs. Each drug was tested in a serial dilution of 7 concentrations, and each two-drug combination was tested with a matrix of 49 conditions (7 x 7) in technical triplicates. The dataset files include the growth rate response of every treatment conditions of all the combinatorial drug screening experiments.

In addition, for 2 of the drug combinations, downstream mechanistic analysis was performed using staining and western blot, and the dataset files include the staining results in terms of positive cell proportion, and raw photo of the chemiluminescent signal detection of every western blot.