Pupae from w1118 flies were collected at various time points between 12h and 96h after puparium formation. Brain tissue was incubated in papain and Liberase protease and mechanically dissociated.
Dmel R6.32
Integration of the data from the different samples was performed on 3,000 highly variable genes selected across all samples. Mitochondrial genes, ribosomal protein genes, genes encoding heat-shock proteins and genes from oxidative phosphorylation complexes were excluded from this set. The integrated dataset was scaled and used for principal component analysis, and the first 200 PCs were used for graph-based clustering.
Reads were processed using Cell Ranger v3.1.0 with default parameters. They were aligned to the Drosophila melanogaster reference genome BDGP 6.29. For quality filtering, cells with less than 2,000 transcripts or more than 20,000 transcripts, cells with more than 10% of mitochondrial transcripts, and cells with more than 3 transcripts aligned to male-specific genes, were excluded.
