Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic pain

Despite wide applications in tissue mapping and vastly improved imaging and omics technologies, spatial, genome-wide assays of gene expression are yet to reliably achieve the resolution and sensitivity approaching dissociative single-cell RNA sequencing. Here, we introduce Pixel-seq, a spatial barcoding method using “continuous” polony gels of ≤ 1 µm feature resolution for capturing tissue RNAs and precise aggregation of mapped transcripts into individual cells. The single-cell assay was demonstrated on mapping the most common brain structures, neuron layers and clusters, creating a three-dimensional atlas of the mouse parabrachial nucleus, and discovering neuropathic pain-associated gene regulation, glial transcriptomic dynamics, and cell-cell communication in the homeostatic adult brain. Our results highlight the necessity of the non-dissociative single-cell sequencing for mapping structural and functional heterogeneity in tissues. 1. Method demonstration (1 mouse olfactory bulb section); 2. PBN structure and activity mapping (7 mouse PBN sections)