Sci-Space E14 Mouse Embryo Data

Spatial patterns of gene expression span many scales, and are shaped by both local (e.g. cell-cell interactions) and global (e.g. tissue, organ) context. However, most in situ methods for profiling gene expression either average local contexts or are restricted to limited fields of view. Here we introduce sci-Space, a scale-flexible method that retains single cell resolution while resolving spatial heterogeneity in gene expression at larger scales. As a proof-of-concept, we apply sci-Space to the developing mouse embryo (E14), capturing the approximate spatial coordinates of profiled cells from whole embryo serial sections. Combinatorially indexed single cell TNA sequencing libraries. Each read contains a combination of PCR indices and a 3-prime barcode that uniquely identify the reads from a single cell. Sequenced molecules consist of both barcoded cDNA and barcoded synthetic hash-oligo molecules used to mark the spatial position from which a cell is derrived.