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Related Experiment Video

Updated: Jun 30, 2025

Robust 3D DNA FISH Using Directly Labeled Probes

Robust 3D DNA FISH Using Directly Labeled Probes

Published on: August 15, 2013

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

Xinrui Zhou¹, Wan Yi Seow¹, Norbert Ha¹

¹Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore.

Nature Communications

|March 16, 2024

Summary

This summary is machine-generated.

We developed Fluorescence In Situ Hybridization of Cellular HeterogeneIty and gene expression Programs (FISHnCHIPs), a sensitive and efficient method for spatial omics. FISHnCHIPs enables rapid, high-resolution cell typing in tissues for research and diagnostics.

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Last Updated: Jun 30, 2025

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Area of Science:

Biomedical research
Molecular biology
Genomics

Background:

Existing spatial omics technologies are expensive and time-consuming.
High-dimensional, spatially resolved tissue analysis is crucial for research and diagnostics.

Purpose of the Study:

To introduce Fluorescence In Situ Hybridization of Cellular HeterogeneIty and gene expression Programs (FISHnCHIPs) for sensitive in situ cell type and gene expression profiling.
To overcome limitations of current spatial omics technologies.

Main Methods:

FISHnCHIPs simultaneously images ~2-35 co-expressed genes clustered into modules.
It achieves high sensitivity and spatial resolution comparable to single-gene FISH.
The method allows for high-speed, large field-of-view tissue profiling.

Main Results:

FISHnCHIPs demonstrated ~2-20-fold higher sensitivity than conventional FISH.
Up to 53 modules were imaged in mouse kidney and brain tissues.
Spatially restricted cancer-associated fibroblasts were identified in colorectal cancer biopsies.

Conclusions:

FISHnCHIPs provides a fast, robust, and scalable solution for cell typing in tissues.
This technology advances the study of tissues in normal physiology and disease pathogenesis.
FISHnCHIPs has significant implications for biomedical research and diagnostics.