This dataset covers single-cell RNA-seq from Hand-GFP transgenic Drosophila lines. Hand is a well-known key transcription factor for cardiogenesis, hemopoiesis and muscle development in Drosophila (Han and Olson, 2005; McFadden et al., 2000). It is highly expressed in fly heart cells across all developmental stages, from embryo through to adult. A total of 34,369 GFP positive cells were obtained from more than 3,000 Hand-GFP embryos; the cells were collected over five consecutive developmental phases known to be critical in fly heart development (embryonic stage 13, 14 early, 14 late, 15, and 16). Even though known for its high expression in fly heart, lower levels of expression in other tissues have been found. Interestingly, in addition to the known Hand expression in heart, muscle, lymph glands, nephrocytes, gut and nervous system cells (Kölsch and Paululat, 2002), our single-cell RNA-seq data revealed Hand expression in fat body, trachea, blood and salivary gland. The data provided here covers the developmental patterns within our model, and used 10X Genomics to assay gene expression in Hand-GFP positive cells representing the nine different tissue types.