Deterministic Genetic Barcoding for Multiplexed Behavioral and Single Cell Transcriptomic Studies

We describe a straightforward genetic barcoding approach that takes advantage of the powerful genetic tools available in Drosophila to allow in vivo tagging of defined cell populations. This method, called Targeted Genetically-Encoded Multiplexing (TaG-EM), involves inserting a DNA barcode just upstream of the poly-adenylation site in a Gal4-inducible UAS-GFP construct, so that the barcode sequence can be read out during single cell sequencing, labeling a cell population of interest. By creating many such independently barcoded fly strains, TaG-EM will enable a number of potential applications that will improve the quality and information content of single cell transcriptomic data including positive identification of cell types in cell atlas projects and barcoding of experimental timepoints, conditions, and replicates. Furthermore, we demonstrate that the barcodes from TaG-EM fly lines can be read out using next-generation sequencing to facilitate population-scale behavioral measurements. Thus, TaG-EM has the potential to enable large-scale behavioral screens in addition to improving the ability to reliably annotate cell atlas data, expanding the scope and improving the robustness of single cell transcriptomic experiments.