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Understanding the spatial gene expression and regulation in the heart is key to uncovering its developmental and physiological processes, during homeostasis and disease. Numerous techniques exist to gain gene expression and regulation information in organs such as the heart, but few utilize intuitive true-to-life three-dimensional representations to analyze and visualise results. Here we combined transcriptomics with 3D-modelling to interrogate spatial gene expression in the mammalian heart. For this, we microdissected and sequenced transcriptome-wide 18 anatomical sections of the adult mouse heart. Our study has unveiled known and novel genes that display complex spatial expression in the heart sub-compartments. We have also created 3D-cardiomics, an interface for spatial transcriptome analysis and visualization that allows the easy exploration of these data in a 3D model of the heart. 3D-cardiomics is accessible from http://3d-cardiomics.erc.monash.edu/.

Understanding spatial gene expression and regulation is key to uncovering developmental and physiological processes, during homeostasis and disease. Numerous techniques exist to gain gene expression and regulation information, but very few utilise intuitive true-to-life three-dimensional representations to analyze and visualize results. Here we combined spatial transcriptomics with 3D modelling to represent and interrogate, transcriptome-wide, three-dimensional gene expression and location in the mouse adult heart. Our study has unveiled specific subsets of genes that display complex spatial expression in organ sub-compartments. Also, we created a web-based user interface for spatial transcriptome analysis and visualization. The application may be accessed fromhttp://3d-cardiomics.erc.monash.edu/.