Continuous Polony Gels for Tissue Mapping with High Resolution and RNA Capture Efficiency

Current technologies for acquiring spatial transcript information from tissue sections rely on either RNA probes or spatial barcodes. The former methods require a priori knowledge for probeset formulation; the latter have yet to achieve single cell resolution and/or transcript capture efficiencies approaching dissociative, single-cell methods. Here, we describe a novel spatial transcriptome assay called p olony (or DNA cluster)- i nde xe d l ibrary-sequencing (PIXEL-seq). It improves upon other spatial barcoding methods by employing “continuous” polony oligos arrayed across a customized gel surface. In terms of assay performance, PIXEL-seq attains ≤ 1 µm resolution and captures >1,000 unique molecular identifiers/10×10 µm 2 . In other words, this global, naive platform achieves subcellular spatial transcriptome mapping while maintaining high transcript capture efficiencies.