Spatial transcriptomics in adultDrosophilareveals new cell types in the brain and identifies subcellular mRNA patterns in muscles

Recently, we have achieved a significant milestone with the creation of the Fly Cell Atlas. This single-nuclei atlas encompasses the entire fly, covering the entire head and body, in addition to all major organs. This atlas catalogs hundreds to thousands of cell types, of which we annotated 250. This still leaves many clusters to be fully characterized, in particular in the brain. Furthermore, with single-nuclei sequencing, all information about the spatial location of the cells and of the mRNAs within these cells is lost. Here, we provide a solution to this problem. In a proof of concept study, we have applied spatial transcriptomics using a selected gene panel to pinpoint the locations of 150 mRNA species in the adult fly. This enabled us to map unknown cell types identified in the Fly Cell Atlas to their spatial locations in the brain. Additionally, spatial transcriptomics discovered interesting principles of mRNA localization in large crowded muscle cells that may spark future mechanistic investigations. Furthermore, we present a set of computational tools that will allow for easier integration of spatial transcriptomics and single-cell datasets.