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Related Experiment Video

Updated: Jan 16, 2026

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

Published on: May 23, 2018

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.

|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.

Keywords:

high content CRISPR screen highly multiplexed RNA imaging spatial transcriptomics

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Last Updated: Jan 16, 2026

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

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Published on: May 23, 2018

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Published on: January 10, 2019

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

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.