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

Spatially resolved transcriptomics is revolutionizing our understanding of complex tissues, but scaling these ap-proaches to multiple tissue sections and three-dimensional tissue reconstruction remains challenging and cost prohibitive. 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 three-dimensional view from multiple consecutive sections, revealing gene expression heterogeneity throughout the tissue.

Automated summary

This study presents a low-cost strategy for manufacturing molecularly double-barcoded DNA arrays, enabling large-scale spatially resolved transcriptomics studies. It reveals gene expression heterogeneity throughout the tissue by applying this technique to spatially resolve gene expression in human brain organoids.