Spatial Genomics for in situ single cell expression analysis in the brain

Summary Identifying the spatial organization of tissues at cellular resolution from single cell gene expression profiles is essential to understanding neurological systemsWe have developed a spatial genomics approach that allows in situD multiplexed imaging of many genes in single cells called sequential Fluorescence in situ hybridizationseqFISHThis technology can profile transcriptional states of single cells directly in their native tissue context with up togenes multiplexed with single molecule sensitivity on each geneWe have demonstrated overcells profiled in mouse brain slicesThis SBIR project will be focused on the designproduction and optimization of an instrument that allows hundreds of genes to be multiplexed and imaged in single cells within their native tissue contextThe resulting machine will be commercially launched and targeted to imaging or sequencing cores at research institutionsWe will design the hardwarecode the control softwareand build the prototype instrumentWe will engineer the hardware component including automated fluidics and multiple camera imaging system with a parallel effort to develop software controls as well as integrated analysis toolsIn phase IIwe will beta test the instrumentgenerate probe sets for gene panels targeting different brain samplesand receive valuable feedback from users and optimize our instrument design Narrative A major challenge of the BRAIN initiative and international Human Cell Atlas project is to identifying distinct cell populations in the brain within their native spatial environmentAddressing this challenge is essential not only to fundamental biological questions of understanding how different cell types interact to form neural circuitsbut also essential in investigating mechanisms of human diseases where small subpopulations of cellssuch as microglialplay pivotal rolesWe have developed an in situD multiplexed imaging method called sequential Fluorescence in situ hybridizationseqFISHthat can profile transcriptional states of single cells directly in a mouse coronal section with up togenes multiplexed in the hippocampus and the cortexShah et alNeuronFrieda et alNatureDelivering this technology as a robust platform that can be used by neuroscientists would enable breakthrough discoveries and treatment optionsTo make this technology available for a broad range of users and customersthis phase I SBIR project will be focused on the designproduction and optimization of an instrument called seqFISHand the parallel development of the control software to operate the seqFISH