Derived data and figure source data for multi-cohort transcriptomic analysis of AR-indifferent resistant prostate cancer states

This dataset accompanies the manuscript “Multi-cohort transcriptomic evidence for convergence toward AR-indifferent resistant states in prostate cancer.” It contains summary supplementary tables, complete gene-set registries, sample-level and robustness outputs, negative-control outputs, and source data used to generate the main and supplementary figures. All files are derived from publicly available processed transcriptomic resources, including cBioPortal, the Gene Expression Omnibus datasets GSE126078 and GSE137829, UCSC Xena, and DepMap Public 26Q1. No controlled-access raw sequencing data, identifiable patient information, or newly collected human specimens are included. The deposited files support reproducibility of the rank-based signature scoring, cohort and phenotype comparisons, patient-level robustness analyses, leave-component-out analyses, negative-control analyses, bulk confounding analyses, marker-inferred epithelial-compartment analyses, and DepMap model-system orientation. Public database source files are not redistributed in this record. The accompanying README.md and the manifest within Figure_Source_Data.zip describe the contents, figure mappings, source roles, and file-verification status. Analysis code and computational environment files are available in a separate Zenodo software record at https://doi.org/10.5281/zenodo.21884065. This release adds derived data and source data for the paired longitudinal analyses incorporated into the revised manuscript. The update includes paired pre- and post-neoadjuvant androgen deprivation therapy (ADT) analyses in GSE111177, directional replication in GSE150368, Figure 6 source data, Supplementary Table 8 source data, and Supplementary Data 4 containing longitudinal paired scores. The transcriptomic convergence framework and signature definitions are unchanged from version 1.0.0. These longitudinal analyses provide treatment-associated longitudinal support for movement along the fixed transcriptomic coordinate but do not establish causal treatment-induced transition, prognostic utility, or treatment-response prediction.