WESTERN DIET AND GAMMA-IR, BUT NOT SIMGCRSIM, ARE ASSOCIATED WITH GREATER SEX-SPECIFIC LIVER CARCINOGENESIS IN AGING C57BL/6J MICE: code and data for reproducing the results

This deposit contains the code and processed data needed to reproduce the transcriptomic and pathology analyses and figures associated with the manuscript "WESTERN DIET AND GAMMA-IR, BUT NOT SIMGCRSIM, ARE ASSOCIATED WITH GREATER SEX-SPECIFIC LIVER CARCINOGENESIS IN AGING C57BL/6J MICE" (Davitavyan et al.; corresponding author D. A. Goukassian), submitted to Science Advances. The study is a lifetime investigation of how diet and space-relevant ionizing radiation affect liver carcinogenesis in male and female C57BL/6J mice. At 90 days of age, animals received 100 cGy ¹³⁷Cs gamma irradiation (γ-IR) or 50 cGy simplified galactic cosmic ray simulation (simGCRsim) on a normal diet, or a Western diet for 125 days without irradiation. Livers were collected for bulk RNA-seq at 118, 455 and 530 days of age (89 samples after resolving duplicates across two sequencing runs: 45 male, 44 female). Animals were followed for neoplasm development to 750 days (males) and 640 days (females). The accompanying analysis covers RUVSeq normalisation and DESeq2 differential expression, self-organizing-map (oposSOM R package) transcriptomic portraits with spot-level functional enrichment, independent component analysis, gene set Z-score comparisons, TCseq temporal clustering, sex-biased and disease-related gene set mapping, and neoplasm incidence analysis. The deposit includes the R Markdown analysis script (Mice_Liver_Transcriptomics_Analysis.Rmd), input tables (STAR gene counts, sample metadata, RNA integrity numbers, gene set files), the trained SOM environment and complete oposSOM output, and the figures and result tables produced by the script. Analyses were run in R 4.4.2; package versions and instructions for running the script are listed in the README. Raw and processed sequencing data are available in NCBI GEO under accession GSE322758. This work was supported by NASA Human Research Program grants 80NSSC19K1079 and 80NSSC21K0549, American Heart Association Career Development Award 24CDA1269532, and Higher Education and Science Committee of the Republic of Armenia grants 24RL-1F029, 25FAST-1F004, 21AG-1F021 and 24AA-1F033.