Integration of single-cell and spatial transcriptomics by SEU-TCA reveals the spatial origin of early cardiac progenitors.

Obtaining single-cell spatial information remains a challenge in spatial transcriptomics. Here we develop SEU-TCA, a method that leverages transfer component analysis to improve single-cell spatial mapping accuracy. Application to multiple single-cell and spatial transcriptomic datasets shows superior performance in spatial deconvolution and cell mapping. Using SEU-TCA, we explore spatial gene expression and regulon activity during mouse gastrulation and identify anterior second heart field progenitors regulated by Irx1. Functional experiments reveal that Irx1 deletion disrupts anterior second heart field development and causes ventricular septal defects, underscoring SEU-TCA's potential for advancing developmental biology research.