A single-cell transcriptome atlas of the ageing Drosophila brain

The diversity of cell types and regulatory states in the brain, and how these change during ageing, remains largely unknown. We present a single-cell transcriptome atlas of the entire adult Drosophila melanogaster brain sampled across its lifespan. Cell clustering identified 87 initial cell clusters that are further subclustered and validated by targeted cell-sorting. Our data shows high granularity and identifies a wide range of cell types. Gene network analyses using SCENIC revealed regulatory heterogeneity linked to energy consumption. During ageing, RNA content declines exponentially without affecting neuronal identity in old brains. This single-cell brain atlas covers nearly all cells in the normal brain and provides the tools to study cellular diversity alongside other Drosophila and mammalian single-cell datasets in our unique single-cell analysis platform. These results allow comprehensive exploration of all transcriptional states of an entire ageing brain. scRNA-seq (10x Genomics CHROMIUM Single Cell 3’ Solution V2 Chemistry and Drop-seq) of adult brains from Drosophila melanogaster at various ages; SMART-seq2 on FAC-sorted R23E10-Gal4 positive neurons of adult brains from Drosophila melanogaster; Adapted SMART-seq2 on FAC-sorted R23E10-Gal4 positive neurons of adult brains from Drosophila melanogaster; CEL-seq2 on FAC-sorted R23E10-Gal4 positive neurons of adult brains from Drosophila melanogaster; Bulk RNA-seq of adult brains from Drosophila melanogaster; ATAC-seq of young (0 days) and old (50 days) adult brains from Drosophila melanogaster