Control reuse, replication-unit choice, and pseudobulk imbalance constrain inference from public Limosilactobacillus reuteri transcriptomic datasets: analysis code, results, and reproducibility archive

Reproducibility archive supporting the manuscript “Deposit reuse and replication-unit choice dominate apparent host transcriptional responses to Limosilactobacillus reuteri in public datasets.” This archive contains analysis code, derived results, figure-generation scripts, metadata snapshots, gene-set membership files, environment specifications, validation outputs, and manuscript files from an exploratory secondary analysis of publicly available Limosilactobacillus reuteri host-response datasets. The analyses include 30 human enteroid RNA-sequencing libraries, 11,996 retained single cells from eight tumour-bearing mice, 257 conditioned-medium metabolites, and six human disease cohorts. The study evaluates control reuse across GEO accessions, sensitivity to replication-unit choice, expression-level bias in gene-set enrichment, exact-permutation limits with eight animals, pseudobulk cell-count imbalance, metabolite detectability, and cross-disease transcriptomic concordance. No new human participants, human specimens, or animal experiments were involved. Source datasets remain available from their original public repositories. This archive contains derived results and reproducibility materials and should be interpreted together with the accompanying manuscript. CC BY 4.0 applies to original material created for this archive. Third-party datasets, metadata, and reference resources remain subject to the terms of their respective original sources.