Photolabile oligonucleotides combined with topologically imposed light gradients enable spatially resolved single-cell transcriptomics and epigenomics

The organization of cells within a tissue plays a critical role in tuning cellular function. Several methods have recently been developed to capture the transcriptome of cells while retaining spatial information. However, these genome-wide sequencing methods typically lack the spatial resolution of individual cells and are confined to quantifying positional information within predefined lattice locations, thereby failing to capture large sections of a tissue outside these regions. Further, these methods are generally limited to profiling fixed cells with reduced mRNA capture efficiency compared to standard scRNA-seq. In addition, existing methods lack modularity and cross-platform compatibility, thereby limiting most of these techniques from jointly profiling the epigenetic and transcriptomic state of individual cells. To overcome these limitations, we present scSTAMP-seq (single-cell Spatial Transcriptomic And Multiomic Profiling), an approach that employs cholesterol-tagged photolabile oligonucleotides that incorporate into cell membranes, enabling us to "stamp" the position of cells using spatially imposed light gradients prior to tissue dissociation and single-cell sequencing. Applied to live cells, scSTAMP-seq efficiently captures spatially resolved single-cell transcriptomes at high resolution for all cells within a field of view. Further, we demonstrate that light patterning enables dynamic spatial resolution, including the ability to map the position of individual cells. Finally, we show that scSTAMP-seq is modular and can be seamlessly integrated with various downstream single-cell sequencing technologies. We demonstrate this by performing scRNA-seq using plate- and droplet-based methods, and by performing joint epigenome and transcriptome sequencing from the same cell while preserving positional information. Collectively, these results demonstrate that scSTAMP-seq is a sensitive and high-throughput technology for mapping single-cell transcriptomes and epigenomes at the spatial resolution of individual cells.