Systematic cell-type resolved transcriptomes of 8 tissues in 8 lab and wild-derived mouse strains capture global and local expression variation

Mapping genomic variation onto gene expression can illuminate complex traits and disease predisposition. The challenge is resolving strain effects that concentrate in specific cell types and states linked to immune and metabolic traits. The IGVF 8-cube profiled 5.2 million nuclei across eight tissues and all eight Collaborative Cross founder strains, finding that transcriptome variation tracks genetic divergence and is greatest in wild-derived strains.