Tetrathiomolybdate attenuates a DLD-gated copper vulnerability and organ injury in endotoxemic mice: code and data deposition (v1.4.10)

Abstract

Code, data and the submission snapshot for the manuscript "Tetrathiomolybdate attenuates a DLD-gated copper vulnerability and organ injury in endotoxemic mice", submitted to Pharmacological Research. The model is LPS endotoxemia (intraperitoneal LPS 10 mg/kg); bench-recorded group labels in deposited raw files are retained verbatim and mapped to manuscript terminology in the change ledger (Addenda 5 and 8). The deposition contains: (1) a wetlab package with raw evidence (imaging, plate exports, qPCR, western blots with uncropped membranes, modeling records) and SHA-256 manifests; (2) code_and_logs with analysis scripts and run logs; (3) source_data_core tables linking every quantitative claim to deposited files; (4) the Pharmacological Research submission snapshot — manuscript, highlights, cover letter, declaration of interests, ARRIVE 2.0 checklist, supplementary figures S1-S21 with uncropped immunoblot membranes, supplementary tables S1-S16, and the immutable preregistration of the si-DLD × TTM factorial prediction; (5) main figures 1-4 (300/600 dpi, PDF+PNG+TIFF) and the graphical abstract; (6) manifests and a versioned change ledger (CHANGELOG). The copper-DLD model: copper-induced ATP depletion in macrophages, gated by flux through DLD-containing complexes (DLD as a flux node / E3 hub, not a copper-binding site); organ protection by tetrathiomolybdate (TTM) in endotoxemic mice. Version history: v1.4.0-v1.4.2 accompanied a Metabolism submission (superseded). v1.4.3 (2026-10-07) regenerated the main immunoblot quantification (DLD induction 6.42-fold, TTM reversal 78.1%, ANOVA + Tukey), corrected the SuppFigS21 exposure summary and rebuilt the S10 forest. v1.4.4 added the Pharmacological Research snapshot. v1.4.5 synced the snapshots, added uncropped blots, and re-built Supplementary Fig. S14 as a single-page four-panel figure with dot-plot quantification (former bar charts superseded by deposited adjusted statistics; four-group membrane panel moved to Fig. 1I; DLD IHC and H&E panels removed as duplicates of Fig. 2D; panels re-lettered A-D). v1.4.6 fixed the author name (Huangwei Li → Huangwei Lin). v1.4.7 (2026-10-09) reworded one highlights bullet. v1.4.9 (2026-10-12) finalized Supplementary Fig. S14 at submission quality (membrane strips re-cropped from the author's re-exported composite; caption terminology corrected); completed the LPS model-terminology correction across the manuscript, supplementary methods, ARRIVE checklist, all four main figures, the graphical abstract and the supplementary-figure covers (bench-label mapping in CHANGELOG Addenda 5 and 8; public CLP datasets GSE342888/GSE313149 unchanged by design); aligned the author list and the co-first-author and corresponding-author annotations across the manuscript and all supplementary files; restored one Section 2.3 sentence (organ endpoints sampled 7.3-7.5 h after injection, per the deposited animal master list) that had regressed in the word-processor file; and replaced the western-blot display composite raw_WB_20260706/WB5_panel_ATP5A1-ATP5B.tif in the wetlab package by the author's re-export, with the superseded 2026-10-02 panel preserved inside the package under superseded/ with a notice (gray-value workbooks unchanged; all quantitative values identical in every version). Docs, figures, wetlab and manifests packages were refreshed accordingly. Earlier superseded versions remain accessible under their own DOIs. All quantitative claims map to deposited source tables.Funding: NSFC 82660026; Hainan Provincial Natural Science Foundation 825RC864, 825RC856; Hainan Medical University XSTS2025168; Joint Program WSJK2026MS204. v1.4.10 delta (no quantitative value changed in any file): this version propagates two author-side image corrections into the snapshot. (1) Figure 1 in the figures snapshot (PDF/PNG/TIFF) now carries the author's fix of the truncated panel I (immunoblot quantification). (2) Page 16 of the uncropped immunoblot membranes PDF was re-spliced from the updated S14B ATP5A1 membrane-3 acquisition file; the package README and cover letter were refreshed accordingly. The source-data core, wetlab, code-and-logs, CellSystems and manifests packages are byte-identical to v1.4.9. See CHANGELOG_v1.4.10.md (Addenda 11-12) for the full audit trail.