Embryo-scale, single-cell spatial transcriptomics

Localizing gene expression Single-cell RNA sequencing can provide information about cellular relationships based on shared transcriptomes, but most methods lose spatial information. Those methods that do retain spatial information can be limited to a specific set of genes and/or a small area. Srivatsan et al. introduce sci-Space, a spatial transcriptomic method that uses a grid of barcoded oligos on a slide that can be transferred to nuclei of an overlaid frozen tissue section to obtain both the spatial origin and the transcriptome of thousands of single cells per slide. The researchers used sci-Space to create a spatial atlas of mouse E14 sagittal sections, revealing spatially expressed genes across cell types. This application illustrates how sci-Space complements existing approaches in spatial genomics. Science , abb9536, this issue p. 111