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bioRxiv · 10.1101/2023.04.11.536345

Highly sensitive spatial transcriptomics using FISHnCHIPs of multiple co-expressed genes

ZHOU, X.·SEOW, W. Y.·Ha, N.·Cheng, T. H.·Jiang, L.·Boonruangkan, J.·Goh, J. J. L.·Prabhakar, S.·Chou, N.·Chen, K. H.
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Abstract

High-dimensional, spatially resolved analysis of intact tissue samples promises to transform biomedical research and diagnostics, but existing spatial omics technologies are costly and labor-intensive. We present FISHnCHIPs for highly sensitive in situ profiling of cell types and gene expression programs. FISHnCHIPs achieves this by simultaneously imaging [~]2-35 co-expressed genes that are spatially co-localized in tissues, resulting in similar spatial information as single-gene FISH, but at [~]2-20-fold higher sensitivity. Using FISHnCHIPs, we imaged up to 53 gene modules from the mouse kidney and mouse brain, and demonstrated high-speed, large field-of-view profiling of a whole tissue section. FISHnCHIPS also revealed spatially restricted localizations of cancer-associated fibroblasts in a human colorectal cancer biopsy. Overall, FISHnCHIPs enables robust and scalable spatial transcriptomics analysis of tissues with normal physiology or undergoing pathogenesis.

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ZHOU, X., SEOW, W. Y., Ha, N., Cheng, T. H., Jiang, L., Boonruangkan, J., Goh, J. J. L., Prabhakar, S., Chou, N., Chen, K. H.. 2023-04-12. Highly sensitive spatial transcriptomics using FISHnCHIPs of multiple co-expressed genes. https://doi.org/10.1101/2023.04.11.536345

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