Complementary remodeling strategies distinguish human subcutaneous and omental adipose tissue

Reproducibility package for: "Complementary remodeling strategies distinguish human subcutaneous and omental adipose tissue" This deposit contains the de-identified data, analysis code, and supplementary materials required to reproduce all statistics and figures reported in the manuscript. ## Study overview Paired subcutaneous (SAT) and omental visceral (VAT) adipose specimens were analyzed by bulk RNA sequencing (29 specimens from 19 patients, including 10 SAT–VAT pairs), together with an independent histology cohort (n = 30) with baseline CT. The study characterizes depot-specific transcriptional identity (SAT mesenchymal/TBX15–SHOX2 versus VAT mesothelial–stromal/UPK3B) and a storage-versus-scaffold relationship in which omental VAT accommodates more adipose area per unit histological fibrosis than SAT. Ethics: Approved by the Institutional Review Board of Chungbuk National University Hospital (IRB No. CBNU-2025-A-0174). ## Contents - `norm.count.txt` — normalized expression matrix (16,493 gene symbols × 29 samples)- `TableS1–S6*.csv` — supplementary tables (cohort demographics, CT/HU, module definitions, sample flow, storage–scaffold analysis with robustness, external validation)- `reproduce_verify.py` — regenerates every statistic reported in the manuscript- `scaffold_analysis.py`, `scaffold_robustness.py` — storage-versus-scaffold analyses and sensitivity checks- `HU_analysis.py` — CT attenuation analyses- `gtex_validation.py` — external validation against GTEx v8- `sequencing_report/` — Macrogen sequencing and QC reports (TRR report HN00276103; sample and library QC), the primary source for the sequencing methods ## Methods summary RNA sequencing: Agilent SureSelectXT RNA Direct (capture-based, suitable for partially degraded adipose RNA), Illumina paired-end 151 bp, reference genome GRCh38, RefSeq annotation. Differential expression: edgeR with TMM normalization and exactTest. Module scores were computed as the mean of cohort-wide per-gene z-scores. Paired SAT–VAT comparisons used the exact Wilcoxon signed-rank test; mixed-effects models included a patient random intercept. ## External data (not redistributed here) - GTEx v8 adipose gene TPMs (Adipose–Subcutaneous, n = 663; Adipose–Visceral/Omentum, n = 541), obtained from the GTEx Portal- Emont et al. human adipose single-nucleus atlas, obtained from the Single-Cell Portal (SCP1376) and GEO (GSE176171) These datasets are publicly available from their original sources and are not redistributed in this deposit; the analysis scripts provided here reproduce the external-validation results from those sources. ## Notes Patient identifiers are removed; the histology cohort is anonymized (H01–H30). No individually identifiable information is included. License: [선택하신 라이선스 — CC BY 4.0 권장]