Single nucleus RNA sequencing of the cerebral cortex from genetically diverse inbred mouse strains reveals differences in pericyte and endothelial cell composition

Genetic background influences animal behavior and susceptibility to brain diseases. To evaluate how genetic background influences the relative number and/or types of cells in the brain, we performed single nucleus RNA sequencing on 14 genetically distinct collaborative cross (CC) inbred mouse strains. These data comprise over 287,000 nuclei derived from 92 samples across each of the strains. We identified 11 principal cell types and 59 refined cell types in each of the strains. Overall design: We isolated nuclei from the right cortical hemisphere from 92 animals of 14 different CC inbred mouse strains. We performed Split Pool Ligation-based Transcriptome sequencing (SPLiT-seq) using these samples. After processing the data, we had over 287,000 nuclei derived from 92 samples acorss each of the strains.