ArticleNature communications2024
Highly sensitive spatial transcriptomics using FISHnCHIPs of multiple co-expressed genes.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Disruption of hippocampal upstream regulators of mTOR and insulin pathways in Down syndrome with Alzheimer's disease neuropathology: Preliminary observations.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
- CIPHER: An end-to-end framework for designing optimized aggregated spatial transcriptomics experiments.PLoS computational biology · 2026Article
- Review
- Tetrahedral DNA dendritic nanostructure-enhanced FISH for high-speed, sensitive spatial transcriptomics.Nature communications · 2025Article
- Spatially resolved subcellular protein-protein interactomics in drug-perturbed lung-cancer cultures and tissues.Nature biomedical engineering · 2025Article
- Next generation lineage tracing and its applications to unravel development.NPJ systems biology and applications · 2025Review
- Efficient and highly amplified imaging of nucleic acid targets in cellular and histopathological samples with pSABER.Nature methods · 2025Article
- Spatial Single-Cell Mapping of Transcriptional Differences Across Genetic Backgrounds in Mouse Brains.bioRxiv : the preprint server for biology · 2024Article
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Authors and funding
10 authors.
Funding
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 Fluorescence In Situ Hybridization of Cellular HeterogeneIty and gene expression Programs (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 (clustered into modules) that are spatially co-localized in tissues, resulting in similar spatial information as single-gene Fluorescence In Situ Hybridization (FISH), but with ~2-20-fold higher sensitivity. Using FISHnCHIPs, we image up to 53 modules from the mouse kidney and mouse brain, and demonstrate high-speed, large field-of-view profiling of a whole tissue section. FISHnCHIPs also reveals spatially restricted localizations of cancer-associated fibroblasts in a human colorectal cancer biopsy. Overall, FISHnCHIPs enables fast, robust, and scalable cell typing of tissues with normal physiology or undergoing pathogenesis.
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