Reference-gene context reshapes transcriptomic signals across the skeletal-dysplasia landscape

This research compendium accompanies an exploratory study of how reference-gene context changes the interpretation of growth-plate and broader tissue-expression signals across skeletal-dysplasia genes. It contains frozen processed inputs, matched analysis sets, provenance manifests, gene ledgers, derived outputs, reproducible analysis code, and anonymous editable Markdown copies of the manuscript and Supplementary Information prepared for Heredity. The analyses include prespecified genomic-control models; growth-plate and adipose comparisons under a later disease-panel control universe; panel-control source-ledger audits; a residualisation identity check; complete-genome sensitivity; and fixed-design null calibration. Direct contrasts reuse the same cases and are not independent replication. The later panel does not reconstruct the historical diagnostic testing universe, so the results demonstrate sensitivity to reference-gene definition but do not establish tissue specificity, clinical utility, causal ascertainment effects, or validated biological prioritisation. Source accessions and reacquisition information are documented in the archive.