Three-dimensional molecular cartography of human cerebral organoids revealed by double-barcoded spatial transcriptomics

Spatially-resolved transcriptomics methodologies are revolutionizing our understanding of complex tissues, but their elevated costs represent still a bottle-neck for their democratization. In this work we present a low-cost strategy for manufacturing molecularly double-barcoded DNA arrays, enabling large-scale spatially-resolved transcriptomics studies. We applied this technique to spatially resolve gene expression in several human brain organoids, including the reconstruction of a 3-dimensional view from multiple consecutive sections, revealing gene expression divergencies throughout the tissue. Spatial transcriptomics assays based on the use of in-house manufactured double-barcoded DNA arrays.