Reproducibility archive for manuscript 623972: histone-cluster and prespecified ion-channel transcriptomic analyses in endometriosis

Xinyue Cui, Jiaxuan Liu, Shengwu Wang, Huali Xu, Yali Fang, Guiping Wan, Rui Rui, Hong Zhu
2026 · doi:10.5281/zenodo.22097723 · W7204215284
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This reproducibility archive supports revised transcriptomic analyses of endometriosis by providing auditable workflows, pre-specified ion-channel confirmations, and negative results for datasets GSE51981 and GSE153739.

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This document serves as a reproducibility archive for manuscript 623972, providing auditable workflows and data for transcriptomic analyses of histone clusters and ion channels in endometriosis. It includes processed expression datasets from GSE51981 and GSE153739, along with scripts, decision rules, and logs to verify proliferation and menstrual-phase sensitivity results. The archive explicitly excludes legacy differential-expression findings that could not be reproduced through the documented statistical pipeline, ensuring only verified results are considered. This paper is centrally about endometriosis — specifically focusing on the reproducibility of histone-cluster and ion-channel transcriptomic analyses within the disease context.

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Abstract

inal reproducibility archive supporting the revised analysis of manuscript 623972. The archive contains auditable GSE51981 and GSE153739 processed-expression workflows, proliferation and menstrual-phase sensitivity analyses, targeted histone-rich pathway analyses, and a pre-specified confirmatory ion-channel analysis with frozen gene sets and decision rules. It includes input matrices, analysis scripts, exact output tables including negative results, session information, run logs, the pre-specification and deviations log, and SHA256 checksums. Legacy differential-expression results that could not be reproduced from a documented statistical pipeline are not treated as verified findings in the revised manuscript.
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Reproducibility archive for manuscript 623972: histone-cluster and prespecified ion-channel transcriptomic analyses in endometriosis Authors/Creators Description inal reproducibility archive supporting the revised analysis of manuscript 623972. The archive contains auditable GSE51981 and GSE153739 processed-expression workflows, proliferation and menstrual-phase sensitivity analyses, targeted histone-rich pathway analyses, and a pre-specified confirmatory ion-channel analysis with frozen gene sets and decision rules. It includes input matrices, analysis scripts, exact output tables including negative results, session information, run logs, the pre-specification and deviations log, and SHA256 checksums. Legacy differential-expression results that could not be reproduced from a documented statistical pipeline are not treated as verified findings in the revised manuscript. Files 623972_FINAL_REPRODUCIBILITY_ARCHIVE (1).zip Files (74.0 MB) | Name | Size | Download all | |---|---|---| | md5:dbadda7980bf52dd8008e7aa93034979 | 74.0 MB | Preview Download |

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