Single-Cell RNA sequencing of stage 6 Drosophila embryos with 25 enhancer reporter assays

Single-cell RNA sequencing (scRNA-seq) in Drosophila embryos at 2.5 to 3.5 hours after egg lay (corresponding to developmental stages 5 to 7, with a majority of stage 6). The experiments were performed in the nos-phiC31; attP40 fly line containing a reporter construct with the sequence of a candidate enhancer driving the expression of the CD2 reporter gene. scRNA-seq libraries were generated using the 10X 3' end v3.1 kit, with three batches of embryo collection, dissociation, 10X chromium encapsulation, and sequencing performed from the same flies.