Title: Light-Directed Spatial Omics Using Photocleavable Oligonucleotides for Single-Cell and Subcellular Profiling

Abstract: 

The spatial organization of cells within tissues is critical for regulating cellular function, yet most single-cell sequencing approaches require tissue dissociation, resulting in the loss of positional information and limiting our ability to link spatial context with gene expression and epigenetic regulation. To overcome these limitations, I present scSTAMP-seq (single-cell Spatial Transcriptomic And Multiomic Profiling) and icSTAMP-seq (intracellular Spatial Transcriptomic And Multiomic Profiling), a modular light-encoded barcoding strategy that preserves spatial information. 

 

scSTAMP-seq labels live or fixed cells with cholesterol-conjugated, photocleavable hashtag oligonucleotides (PHO) that incorporate into cell membranes, followed by patterned light exposure that enables “stamping” the spatial coordinates onto individual cells prior to sample dissociation and single-cell sequencing, thereby enabling flexible, high-resolution encoding of spatial information across fields of view using discrete or gradient-based illumination patterns. 

 

Extending beyond single-cell spatial profiling, I introduce icSTAMP-seq, which targets subcellular components through modifications to the labeling strategy. icSTAMP-seq directly labels mRNA and genomic DNA molecules using a set of oligonucleotides. We demonstrate that icSTAMP-seq enables iterative rounds of labeling, leading to an exponential increase in spatial resolution. In addition, icSTAMP-seq enable