A dataset of sex-specific transcriptome divergence and evolutionary patterns in the house mouse

Mouse featureCounts. This dataset comprises two distinct sets of gene expression count data for Mus musculus, generated using featureCounts (v1.6.3) against the Ensembl v110 annotation of protein-coding and lncRNA genes. The primary dataset includes 432 samples from 54 adults representing three taxa: France (FR, M.m.domesticus), Kazakhstan (KA, M.m.musculus), and Spain (SP, M.spretus). It profiles gonadal organs (testis, epididymis, vas deferens; ovary, uterus, oviduct) and five somatic tissues (brain, heart, liver, kidney, mammary gland). The secondary dataset contains 224 samples from 24 male mice of three M. m. domesticus populations (GE, FR, IR), focusing on testis and nine somatic organs (brain, lung, spleen, gut, kidney, thyroid, heart, muscle, liver).DE gene analysis. This dataset provides comprehensive sets of DE genes, identified through analysis with both edgeR (v3.30.3) and DESeq2 (v1.25.1). For Dataset I, DE genes were identified from comparisons across sexes and all tissues, encompassing both intra-subspecies comparisons (FR vs. KA) and inter-species comparisons (FR-KA vs. SP). For Dataset II, the analysis focused on all available tissues from male mice, identifying DE genes for comparisons at shorter evolutionary timescales (FR vs. GE) and broader lineage comparisons (FR-GE vs. IR).Sex biased gene analysis. This dataset contains sex-biased genes identified using edgeR based on the Dataset I, which includes samples from both sexes. Sex-biased expression genes were systematically identified for each of the three populations (FR, KA, SP), separately for each organ and each gene type.