show Abstracthide AbstractIllumina RNA-Seq data were collected from outbred individuals from two Mus musculus subspecies, M. m. domesticus (from France) and M. m. musculus (from Kazakhstan) as well as two sister species, M. spretus and M. spicilegus. As non-gonadal organs we included brain, heart, kidney, liver, and mammary gland. As gonadal organs we chose ovary, oviduct, and uterus from females and testis, epididymis, and vas deferens from males. All organs were always retrieved from the same individuals, allowing expression comparisons between organs within each individual. Details can be found in the annotation of each sample and the manuscript.