Single Cell Spatial Transcriptomics Shared Instrument at the BCM Core Facility

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Abstract Single-cell omics is a rapidly growing new field that provides many advantages over traditional ‘bulk’ tissue profiling methods, such as the ability to resolve intratissue heterogeneity in cell types, profile disease microenvironments, and study rare subpopulations. However, one of the major drawbacks of current single-cell transcriptome technologies is that they require the isolation of single cells, resulting in the loss of spatial information. To address this issue, spatial single-cell transcriptomics technologies have been recently developed, which will enable many new research opportunities. The requested instrument, the MERSCOPE from Vizgen, is currently the only commercial platform for the recently developed multiplexed error-robust fluorescence in situ hybridization (MERFISH) technology that allows in situ transcriptome profiling at single cell resolution. By utilizing error-robust and error-correcting encoding schemes, MERFISH enables massively multiplexed single-molecule RNA imaging with high sensitivity and accuracy. The shared MERSCOPE instrument will be placed at and administrated by the established BCM Single Cell Genomics Core (SCGC) to ensure smooth operation and easy access. We have identified 16 research groups at BCM as users. Together, these groups have 41 active research projects funded by the NIH and will use 90% of the capacity of the instrument. The research focuses of these projects are highly diverse, and they are funded by fifteen institutes at the NIH, including the NICHD, NIAMS, NIDC, NCATS, NIDDK, NEI, NCI, NIA, NIGMS, NHLBI, NHGRI, NINDS, NIAID, NIEHS, and NIMDH. As the participating PIs are all engaged in both basic and clinical research, we believe the introduction of this new instrument will have direct, broad, and immediate impact on many medically relevant fields.