Dendrimeric DNA Coordinate Barcoding Design for Spatial RNA Sequencing

Abstract

AbstractSpatially resolved transcriptomic technologies show promise in revealing complex pathophysiological processes, but developing sensitive, high-resolution, and cost-effective methodology is challenging. Here, we report adendrimeric DNAcoordinate barcodingdesign for spatialRNAsequencing (Decoder-seq). This technology combined dendrimeric nano-substrates with microfluidic coordinate barcoding to generate high-density spatial DNA arrays with deterministically combinatorial barcodes in a resolution-flexible and cost-effective manner (∼$0.5/mm2). Decoder-seq achieved high RNA capture efficiency, ∼68.9% that ofin situsequencing, and enhanced the detection of lowly expressed genes by ∼five-fold compared to 10× Visium. Decoder-seq visualized a spatial single-cell atlas of mouse hippocampus at near-cellular resolution (15 μm) and revealed dendrite-enriched mRNAs. Application to renal cancers dissected the heterogeneous tumor microenvironment of two subtypes, and identified spatial gradient expressed genes with the potential in predicting tumor prognosis and progression. Decoder-seq is compatible with sensitivity, resolution, and cost, making spatial transcriptomic analysis accessible to wider biomedical applications and researchers.