Reproducibility archive for "A Lipoylation–PDH–TCA Transcriptional Deficit in the Alzheimer's Disease Cortex: Donor-Level Multi-Cohort Evidence With Neuronal-Composition, Disease-Specificity and Matched-Null Controls"

Reproducibility archive for the manuscript listed above, submitted to the Journal of Molecular Neuroscience (submission bb75a07b-54c2-48da-9527-581d2fc410b7). The archive contains the single results table to which every number in the manuscript, its figures and its supplementary material resolves, together with the prespecified gene sets, the analysis plan with its primary, secondary, exploratory and removed tiers, the minimum detectable effect tables that accompany every null result, a table of what the study does not measure, all twenty-four supplementary tables in machine-readable form, and the source data for the supplementary figures. It also contains runnable R scripts that reproduce the analyses performed during revision directly from public data: donor-level re-estimation of the cohorts with repeated measures per donor, areas under the receiver operating characteristic curve with confidence intervals, and the four-cohort cross-cohort meta-analysis at donor level. All primary data are public. Transcriptomic and single-nucleus datasets are available from NCBI GEO under GSE157827, GSE138852, GSE161355, GSE33000, GSE5281, GSE122063, GSE132903 and GSE48350. NHANES 2011-2014 is available from the CDC. No new data were generated and no individual-level restricted data were used. Raw expression matrices are not included because they exceed the size limit and are available from the accessions listed above.