Reads were processed using CellRanger (10x Genomics) v2.1.0 for the adult stage and v3.0.1 for the pupal stages. They were mapped to the Drosophila melanogaster reference genome BDGP 6.88. For quality filtering, cells with less than 1,000 UMIs, more than 20,000 UMIs, or with more than 10% of UMIs corresponding to mitochondrial genes, were excluded. Further, genes that were expressed in less than 3 cells across all experiments for a given stage were excluded as well. Dimensionality reduction was performed with Seurat v3.0.0.9 by computing 120 principal components with a resolution of 10 for the adult stage, or a resolution of 6 for the pupal stages.