Mast cells (MCs) are tissue-resident immune cells which exhibit homeostatic and neuron-associated functions. Here we combined whole-tissue imaging and single-cell RNA sequencing datasets to generate a pan-organ analysis of MCs in mice and humans at steady state. In mice, we identify two mutually exclusive MC populations, MrgprB2⁺ connective tissue-type MCs and MrgprB2^neg mucosal-type MCs, with specific transcriptomic core signatures. While MrgprB2⁺ MCs develop in-utero independently of the bone marrow, MrgprB2^neg MCs develop after birth and are renewed by bone marrow progenitors. In humans, we unbiasedly identify 7 MC subsets (MC1 to 7) distributed across 12 organs with different transcriptomic core signatures. MC1 are preferentially enriched in the bladder, MC2 in the lungs, and MC4, MC6 and MC7 in the skin. Conversely, MC3 and MC5 are shared by most organs, but not skin. This comprehensive analysis offers valuable insights into the natural diversity of MC subtypes in both mice and humans.

Single cell datasets generated with 10X plateform at laboratory aggregated with publicly available datasets.

Tar archives contain raw sequencing data in fastq format.

Rds file contains processed Seurat R objects.