10X Chromium single-cell RNA sequencing of the hematopoietic system and niche cells of young and old female individuals from four distinct mouse species

The aim of this study was to analyse the evolutionary conservation or divergence of the aging murine hematopoietic system, which includes hematopoietic stem and progenitor cells (HSPCs) and stromal cells from the hematopoietic niche. The animals used were young (10-13 weeks) and old (84-109 weeks) female individuals from four mouse species: Mus musculus strains C57BL/6J or C57BL/6J-Ly5.1 (BL6), Mus musculus castaneus (CAST/EiJ), Mus spretus (SPRET/EiJ), and Mus caroli (CAROLI/EiJ). We isolated HSPC and niche cells from each animal and performed scRNAseq using the 10X Genomics platform. For alignment, we generated a reference genome based on the mm10 genome masked with Ns in positions of SNVs between species.