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Updated: Jan 16, 2026
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An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing
Published on: May 23, 2018
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Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution.
Yubao Cheng1, Shengyuan Dang1, Yuan Zhang1
1Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
Cell
|October 2, 2025
Summary
Researchers developed RAEFISH, a novel spatial transcriptomics method providing whole-genome coverage and single-molecule resolution. This technology enables high-resolution mapping of gene expression in intact tissues, advancing cellular and tissue analysis.
Area of Science:
- Molecular Biology
- Genomics
- Biotechnology
Background:
- Spatial transcriptomics advances cellular and tissue understanding.
- Current methods face limitations in transcriptomic coverage and spatial resolution.
- Unbiased, high-resolution transcriptomic analysis remains a challenge.
Purpose of the Study:
- To develop a novel spatial transcriptomics method with enhanced coverage and resolution.
- To enable unbiased, hypothesis-free transcriptomic analyses in intact tissues.
- To profile gene expression at single-molecule resolution across the whole genome.
Main Methods:
- Developed reverse-padlock amplicon-encoding fluorescence in situ hybridization (RAEFISH).
- RAEFISH is an image-based spatial transcriptomics technique.
- Applied RAEFISH to intact human and mouse tissues for transcript profiling.
Main Results:
- Achieved whole-genome coverage and single-molecule resolution in situ.
- Demonstrated spatial profiling of ~23,000 human or ~22,000 mouse genes.
- Revealed transcript localization, cell-type-specific transcriptomes, and gene programs for cell interactions.
- Adapted RAEFISH for spatial readout of guide RNAs in CRISPR screens.
Conclusions:
- RAEFISH offers a broadly applicable technology for high-coverage, high-resolution spatial RNA profiling.
- Enables detailed analysis of native and engineered RNAs in diverse biomedical contexts.
- Facilitates advancements in understanding cellular function, organization, and interactions.
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