Single-cell RNA-seq of Drosophila melanogaster male late third instar larval gonads

The male larval gonad is a complex tissue made up of multiple cell types including germ cells and somatic cells. It is also a key developmental stage with the germline undergoing spermatogenesis. The diversity of cell types and transcriptional regulation of the developing gonad has only been broadly described. In order to get single cell resolution, we profiled late third instar larval testes of a reference Drosophila melanogaster genotype, w[1118] using single-cell RNA-Seq (scRNA-Seq). We identified and annotated 9 cell types including 4 stages of the germ cell lineage, and provide transcriptional profiles for each cell type. Overall design: We generated late third instar larval testes scRNA-Seq profiles in biological quadruplicate pools on the 10X Chromium System (10X Genomics, Pleasanton, CA) with the v2 chemistry. We sequenced (Read1=26 bp, Read2=98 bp and Readi7=8 bp) on a Illumina HiSeq 2500 (Illumina, San Diego, CA).