An embryonic stage 17 single cell atlas from Drosophila melanogaster

A major driver of neural circuit complexity is cellular heterogeneity. We sought to profile all of the neural cell types in the Drosophila embryo at stage 17, a period of rapid synapse and circuit formation in the central nervous system. To do so, we performed whole embryo dissociations of Drosophila embryos followed by single cell RNA sequencing. We then computationally segregated neural cell types based on known gene expression for all neurons (elav) and glia (repo). We hope that this dataset will serve as a community resource for other researchers interested in the molecular determinants of circuit complexity. We dissociated a 50-100 µl pool of surface-sterilized Drosophila embryos (stage 17, 17-18.5 hours after egg laying) in C+G medium using a dounce homogenizer. Cells were then washed and filtered with 40 µm cell strainer. The concentration of viable cells was quantified with Trypan blue using a TC20 automated cell counter. Samples with a minimum viability of 80% were then diluted to 1000 cells/ µl in 1X PBS supplemented with .04% BSA and sequenced using the 10X NextGem v3.1 single cell platform.