A single-cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain

To understand the cellular basis of the immune compartment of the zebrafish brain we have established reliable protocols for dissociation and prospective isolation of brain leukocytes, using fluorescent transgenic lines. By combining this approach with single-cell RNA sequencing, we have generated a gene expression atlas composed of the distinct immune cells present in the homeostatic brain. These analyses revealed the presence of subpopulations of mononuclear phagocytes and other leukocytes, including cell types that have not been -or have been poorly- characterized so far. Here, we present the characterization of a new mononuclear phagocyte population that represents an important fraction among all brain leukocytes. Adult brain single-cell suspensions were prepared from adult Tg(p2ry12:GFP; cd45:DsRed) fish (n=3) and a total of 14,000 cd45:DsRed+ cells were processed for single-cell profiling using the 10x Genomics platform.