Data from: Patient-derived organoids from metastatic colorectal cancer mirror tumor heterogeneity and predict patient survival and drug sensitivity

Datasets Data S1 to S5 are generated in the study “Patient-derived organoids from metastatic colorectal cancer mirror tumor heterogeneity and predict patient survival and drug sensitivity”. The data originate from patient-derived organoids (PDOs) and corresponding colorectal liver metastases (CRLMs) and include genomic, transcriptomic, proteomic, and pharmacological measurements. All datasets are linked through a common sample_id, enabling cross-referencing between molecular, phenotypic, and drug response data from the same samples.

Data S1 – Somatic mutation profiles
Targeted sequencing results from a custom 20-gene panel in PDOs and matched tumor tissues. Each row represents a detected variant. Columns include: sample_id, patient, sample_type, chromosome, position, ref, alt, n_ref_count, n_alt_count, t_ref_count, t_alt_count, maf (mutant allele fraction), filter, gene, func, syn, and AAChange (variant annotation including transcript, exon, nucleotide and amino acid change).

Data S2 – RNA sequencing gene expression counts
Gene-level RNA sequencing count matrix of PDO samples. Rows correspond to genes and columns correspond to PDO sample_id. Columns include: ensembl_gene_id, entrezgene_id, hgnc_symbol, followed by columns representing individual PDO samples containing raw read counts mapped to each gene.

Data S3 – Protein expression from multiplex immunohistochemistry
Quantitative protein expression measurements obtained from multiplex immunohistochemistry (mIHC) analysis of PDO samples. Each row represents one protein measurement in a given PDO sample. Columns include: sample_id, Prot_marker, mIHC_stain_no (multiplex panel identifier), AB_order (antibody staining order), Fluor (Opal fluorophore), mean_express_PDO (mean fluorescence intensity), area_pixels (analyzed image area), and Slide (slide identifier).

Data S4 – Raw drug sensitivity screening measurements
Primary measurements from medium-throughput drug screening assays performed on PDOs. Each row corresponds to one well measurement in a drug screening plate. Columns include: sample_id, sample_id_drums, run_id, assay_no, library_id, compound_name, compound_fimm, compound_drums, compound_type, concentration, concentration_unit, drow, dcol, plate, signal (raw luminescence), and viability (normalized cell viability).

Data S5 – Drug sensitivity scores (DSS)
Summary matrix of drug response profiles derived from the raw screening measurements in Data S4. Rows correspond to PDO samples and columns correspond to tested compounds and run_ids. Drug names without suffix were caclulated based on the runs indicated in the run_id_harmonize and drugs with suffix _lib1 or _lib2 indicate the drug library and run_id in which the compound was tested for the respective PDO sample. The values represent Drug Sensitivity Scores (DSS), a quantitative metric calculated from dose–response curves that integrates both drug potency and efficacy to summarize the overall sensitivity of each PDO to a given compound.