Context-dependent mitochondrial transcriptional variation in autism cortex

Reproducibility package for an exploratory reappraisal of mitochondrial transcription in autism prefrontal cortex. Version 3.3.0 reconstructs the Liu 2016 publication cohort from GSE51264, GSE59288, and supporting files, then restricts primary inference to 25 ASD and 28 control donors within observed lower-age support. All ASD profiles originated in GSE59288 and all controls in GSE51264, leaving diagnosis confounded with source accession. The package contains ten MitoCarta-derived modules, complete gene membership and hierarchy strings, HC3 standard errors, ±0.5 SD equivalence tests, leave-one-donor-out diagnostics, RIN nonlinear and overlapping-range analyses, near-tied source-metadata perturbations, pseudocount and scoring sensitivities, subgroup distribution tests, respiratory-complex and sub-mitochondrial endpoints, and a literature-defined Anitha electron-transport panel. GSE102741 is retained as an independent low-precision comparison. Its external ASD cortical directions were concordant but imprecise; it is reported separately rather than excluded by a calibration gate or pooled with Liu. Third-party source datasets are not redistributed. The archive contains source URLs and SHA-256 checksums, frozen mappings, numerical results, five main and six supplementary figures, tables, environment files, manuscript snapshots, a 54-reference validated bibliography, and integrity manifests. Code is MIT licensed; author-generated documentation, tables, and figures are CC BY 4.0.