Spatially tuneable multi-omics sequencing using light-driven combinatorial barcoding of molecules in tissues / Multiomic

Mapping the molecular identities and functions of cells alongside their spatial tissue context is key to understanding the complex interplay within and between their tissue neighbourhoods. A wide range of methods enable spatial profiling of regions, some down to the level of individual cells, in their anatomical context, via different barcoding schemes that encode either the location or the identity of target molecules. However, all these technologies face a trade-off between spatial resolution, depth of profiling, and scalability. Here, we present Barcoding by Activated Linkage of Indexes (BALI), a method that uses light to write combinatorial spatial molecular barcodes directly onto target molecules in situ, enabling multi-omics profiling by next generation sequencing. A unique feature of BALI is that the user can define the number, size, and shape of the spatial locations to be interrogated, with the potential to profile millions of distinct regions down to subcellular scale. As a proof of concept, we used BALI to capture the transcriptome, chromatin accessibility, or both, from distinct areas of the mouse brain in single tissue sections, demonstrating strong concordance with publicly available datasets. BALI therefore combines high spatial resolution, high throughput, histological adaptability, and workflow accessibility to enable powerful spatial multi-omics profiling.