PCL-seq: enhanced high-resolution transcriptomic profiling of region of interest in fresh frozen and FFPE tissues

The spatial heterogeneity of gene expression has propelled the development of multiple spatial transcriptomics technologies. Here, we present p hoto c leavage and l igation sequencing (PCL-seq), an method for spatial indexing using a light-controlled DNA labeling strategy on tissue section. PCL-seq uses photocleavable oligonucleotides and ligation adapters to construct transcription profiles of region of interest (ROI), selected by microscopically controlled photo illumination apparatus in tissue sections. Applied to mouse embryos, PCL-seq obtains gene expression matrices that align with spatial locations and competitive data quality, featuring around 1.7×10 ⁵ UMIs and 8,600 genes (irradiation diameter=100µm). PCL-seq can also apply to formalin fixation and paraffin embedding (FFPE) mouse embryo sections, whereas obtained competitive data output and recovered thousands of differentially enriched transcripts from limb and skeleton. Additionally, PCL-seq can achieve subcellular resolution, which was demonstrated for differential expression between nuclear and cytoplasmic. Thus, PCL-seq provides an accessible workflow for spatial transcriptomic analysis in frozen and FFPE tissue at subcellular resolution.