Identifying the spatial organization of tissues at cellular resolution from single cell gene expression profiles is essential to understanding neurological systems. We have developed a spatial genomics approach that allows in situ 3D multiplexed imaging of many genes in single cells called sequential Fluorescence in situ hybridization (seqFISH). This technology can profile transcriptional states of single cells directly in their native tissue context with up to 249 genes multiplexed with single molecule sensitivity on each gene. We have demonstrated over 15,000 cells profiled in mouse brain slices. This SBIR project will be focused on the design, production and optimization of an instrument that allows hundreds of genes to be multiplexed and imaged in single cells within their native tissue context. The resulting machine will be commercially launched and targeted to imaging or sequencing cores at research institutions. We will design the hardware, code the control software, and build the prototype instrument. We 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 tools. In phase II, we will beta-test the instrument, generate probe sets for gene panels targeting different brain samples, and receive valuable feedback from users and optimize our instrument design.
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 environment. Addressing this challenge is essential not only to fundamental biological questions of understanding how different cell types interact to form neural circuits, but also essential in investigating mechanisms of human diseases where small subpopulations of cells, such as microglial, play pivotal roles. We have developed an in situ 3D multiplexed imaging method called sequential Fluorescence in situ hybridization (seqFISH), that can profile transcriptional states of single cells directly in a mouse coronal section with up to 249 genes multiplexed in the hippocampus and the cortex (Shah et al., Neuron 2016, Frieda et al., Nature 2016). Delivering this technology as a robust platform that can be used by neuroscientists would enable breakthrough discoveries and treatment options. To make this technology available for a broad range of users and customers, this phase I SBIR project will be focused on the design, production and optimization of an instrument called seqFISH100 and the parallel development of the control software to operate the seqFISH100.