A cost-effective and flexible workflow for high-resolution spatial transcriptomics in fixed tissue

The spatial heterogeneity of gene expression has driven the development of diverse spatial transcriptomics technologies. Here, we introduce photocleavage and ligation sequencing (PCL-seq), a spatial indexing method based on a light-controlled DNA labeling strategy applied to tissue sections. PCL-seq employs photocleavable oligonucleotides and sequence adapters to construct transcriptional profiles of specific regions of interest (ROIs), designated via microscopically controlled photo-illumination. In frozen mouse embryos, PCL-seq generates spatially aligned gene expression matrices and achieves high-quality data outputs, detecting approximately 170,000 unique molecular identifiers (UMIs) and 8,600 genes (irradiation diameter=100 µm). Moreover, PCL-seq is compatible with formalin-fixed and paraffin-embedded (FFPE) tissues, successfully identifying thousands of differentially enriched transcripts in the digits and vertebrae of FFPE mouse embryo sections. Additionally, PCL-seq achieves subcellular resolution, as demonstrated by differential expression profiling between nuclear and cytoplasmic compartments. These features establish PCL-seq as an accessible and versatile workflow for spatial transcriptomic analyses in both frozen and FFPE tissues at subcellular resolution.