Niche-resolved transcriptional programs and ΔNp63/NRF2-associated enrichment in post-chemoradiation esophageal squamous cell carcinoma

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This public reproducibility record supports the article “Niche-resolved transcriptional programs and ΔNp63/NRF2-associated enrichment in post-chemoradiation esophageal squamous cell carcinoma.” The study analyzed 10x Genomics Visium spatial transcriptomic profiles from 56 post-chemoradiation ESCC surgical specimens across five tissue-microarray slides. The record includes portable analysis code and environment records; exact signature definitions; core-restricted spatial graphs and HMRF assignments; patient-level clinical, niche/pathway, and continuous per-SD Cox result registries; revised Supplementary Data; five deidentified slide-level processed Visium filtered MEX/spatial datasets; a normalized sparse expression matrix; deidentified spot annotations and spatial coordinates; and a deidentified 56-participant clinical/survival/spatial-feature table with a data dictionary. The processed expression package contains 22,572 QC-retained spots; 22,547 had complete HMRF niche assignments and were used in the HMRF domain-level displays. Direct identifiers, re-identification keys, calendar dates, pathology free text, source crosswalks, raw FASTQ, BAM, CLOUPE, source-labelled reports, and serialized analysis objects containing source identifiers are excluded. The patient-level archive retains residual attribute-linkage risk despite removal of direct identifiers; users must not attempt re-identification. The package supports independent reproduction of the reported downstream analyses from the processed count-matrix stage onward. Corresponding investigator: Byoung Hyuck Kim, MD, PhD, Department of Radiation Oncology, Seoul National University College of Medicine and Seoul Metropolitan Government Seoul National University Boramae Medical Center. E-mail: karlly71@snu.ac.kr.

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