Single-cell RNA-seq profiling of early murine adrenogonadal development

To generate a gene expression atlas of early adrenogonadal development, we performed single-cell transcriptome profiling using a high throughput droplet-based system (10X Genomics). Posterior trunks (embryonic day (E) 9.0), urogenital ridges (E10.5 and E11.5), gonads and adrenal glands (E12.5) were harvested from XX and XY Nr5a1 Tg mouse embryos (for adrenals glands, only XY embryos were analyzed). Tissues were enzymatically dissociated and single-cell RNA-Seq libraries were prepared using the Chromium Single Cell 3' v2 Reagent Kit (10x Genomics) according to manufacturer's protocol. Each condition (organ, sex and developmental stage) was performed in two independent replicates.