Source data and reproducible analysis code for multi-cohort and single-cell transcriptomic evaluation of lipoylation/TCA and ATP7A–ATP7B modules in systemic sclerosis-associated interstitial lung disease

This record provides version 1.0.0 of the source data and reproducibility package supporting a multi-cohort and donor-level single-cell transcriptomic evaluation of a prespecified 10-gene lipoylation/TCA module and a two-gene ATP7A–ATP7B module in systemic sclerosis-associated interstitial lung disease (SSc-ILD). The archive contains machine-readable result, sensitivity, quality-control, and audit tables; frozen dataset manifests and analysis configurations; R, Python, and PowerShell source code; Python and R tests; Conda, Python, and R environment records; input hashes and run provenance; analysis-generated figures; and five assembled main figures. Primary GEO files and large rebuildable processed objects are not redistributed. The included manifests retrieve public inputs from GSE248083, GSE231693, GSE48149, GSE81292, GSE40839, GSE231692, GSE128169, and GSE159354. The transcript modules are mechanism-informed expression constructs and are not direct measurements of intracellular copper, copper flux, protein lipoylation, protein aggregation, or cuproptotic cell death. The package is intended to support transparent inspection and reproduction of both positive and negative results rather than diagnostic, prognostic, or therapeutic use. Software is licensed under the MIT License. Derived source tables, figures, configurations, provenance records, and documentation are licensed under Creative Commons Attribution 4.0 International. Third-party GEO data are not included and remain subject to their source repository terms. Funding: The Shenzhen Postdoctoral Research Grant, number 202301548.b.