Supporting data for Thesis "Deciphering the Roles of Somatic XPD Mutations in Bladder Cancer"

This dataset was to characterize clinical and molecular associations of XPD‑mutant bladder tumors and to validate mechanistic consequences experimentally. Major results include impaired DNA‑repair and altered oxidative‑stress/glutathione metabolism, APOBEC‑associated mutagenesis that preferentially targets CTCF binding sites and perturbs TAD boundaries, and enhanced sensitivity of XPD‑deficient cells to ferroptosis. The resource supports discovery, reanalysis, and method development aimed at biomarker evaluation and translational hypothesis testing in BLCA.The data are organized by Chapters, including differential expression results from TCGA BLCA (DESeq2), experimental validation datasets from engineered cell lines (ROS, cell‑cycle, viability, colony‑formation, slot‑blot), CTCF binding‑site mutation and chromatin‑structure analyses (bedtools, FIMO, deepTools outputs and BED/TSV files), and computational pathology/machine‑learning artifacts (CLAM model checkpoints, prediction CSVs, attention weights, and HoVerNet segmentation outputs). Files using TCGA raw data may require access credentials.