Tuesday, April 16, 2024
4/16/2024
Project Summary Recent advances in massively parallel single cell genomic techniques have enabled researchers to study genomic and gene expression in high resolution. However, these techniques do not preserve spatial context of individual cells within the tissue and can bias representation of various cell types due to cell dissociation that is required before application of the techniques. Commercial availability of spatial genomic techniques is sparse. We have recently founded Atlas Bio with the academic inventors of the Slide-Seq technique in order to commercialize the technology. Slide-Seq is an easy-to-use yet sensitive method for measuring spatial transcriptomes in tissue slices, first published in 2019 (Rodriques SG et. al, Science 2019). The technique makes use of a spatially barcoded bead substrate, a set of enzymatic reagents and buffers, and a custom bioinformatics pipeline. It does not require any special instrumentation other than access to a next-generation sequencer. In the first two months of operation of the company, we have successfully replicated the production of the Slide-Seq spatially barcoded substrates and tested their performance. The goal of the proposed Phase II project is to further develop the Slide-Seq technology such that it can be widely disseminated and can be expanded to different applications such as those that require high spatial resolution and detection sensitivity. Specifically, the project will address the scalability, robustness, and manufacturability of the spatially barcoded substrate, which is the key component of the technique. We will also develop solutions to facilitate easy dissemination of the technology through development of consumables, reagent kits, bioinformatics pipeline, and basic data visualization tools, with the goal to lower the barrier of entry to spatial transcriptomic analyses. Lastly, we will work on improving the performance of the spatial transcriptomic technique in terms of spatial resolution and sensitivity, and expand the workable tissue type from fresh frozen to FFPE. By standardizing the technique through commercialization and making it available to a wider audience, we hope to accelerate a new wave of biological discoveries.
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