Mammalian development is driven by key transcriptional regulators that are exquisitely specified in time and space. Insights into the transcriptional programs driving organogenesis have traditionally come from low-plex imaging methods and bulk or single-cell transcriptomics of dissociated embryos. Recent technological advances have made it possible to profile whole transcriptomes of defined areas of tissue while retaining their spatial context. In this webinar, we will discuss the use of the GeoMx® Digital Spatial Profiler and the Mouse Whole Transcriptome Atlas to comprehensively profile the transcriptomes of anatomical substructures of major organs at four time-points in mid-gestation development. Both known and novel cell-type-specific marker genes were detected, and the dynamics of their expression were tracked over time. The full dataset of gene expression data, images, and histological annotations are publicly available as part of NanoString’s Spatial Organ Atlas.