In a publication in Cell, a novel spatiotemporal analytic package is described in which the gene expression can be studied at a subcellular level using a technology platform based on nanoballs distributed on an array with single cell resolution. The platform combines high spatial sensitivity with large field of view, and the publication reports its use to generate a spatially resolved transcriptomic atlas of mouse organogenesis. The study is an international collaboration with researchers from China, USA and Europe, including the Swedish universities KTH-Royal Institute of Technology and Karolinska Institutet at SciLifeLab in Stockholm.

Since the time of Aristotle, understanding how a single totipotent cell, the zygote, develops into a complex organism in a precisely controlled manner, over time and space, is one of the most fascinating scientific challenges. To understand organogenesis, we need to know the expression of all genes in all cells from conception to adulthood. The Stereo-seq technology combines RNA detection sensitivity, resolution and scalability needed to study the fundaments of organogenesis. As a proof of principle, the laboratory mouse was studied revealing the spatial and temporal aspects of embryonic development at a single cell level. The data not only revealed the distribution of gene expression in any cell-type and any time point during development, but also uncovered the molecular program that drives and orchestrates specific developmental events. In summary, a novel technology platform is described that will facilitate in-depth investigation of longstanding questions concerning normal and abnormal mammalian development and provide a platform to study pathogenesis and molecular changes associated with diseases.

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