Protocol for cell-specific RNA expression profiling and lipidomics analyses of Drosophila melanogaster intestinal progenitor cells

Research in the model system Drosophila melanogaster has highlighted the importance of cell-specific in vivo omics analyses to study intestinal epithelial homeostasis. Here, we present an optimized protocol for profiling intestinal progenitor cells (PGs) at the transcriptome and lipidome levels. We describe steps to dissect midguts, isolate fluorescently labeled PGs using fluorescence-activated cell sorting (FACS), and obtain high-quality RNA for library preparation or total lipid extraction for untargeted lipidomics. This protocol yields high-quality transcriptomic and lipidomic data under various experimental conditions. For complete details on the use and execution of this protocol, please refer to Makdissi et al.¹.