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Related Experiment Video

Updated: Mar 19, 2026

Single Cell Analysis Of Transcriptionally Active Alleles By Single Molecule FISH

Single Cell Analysis Of Transcriptionally Active Alleles By Single Molecule FISH

Published on: September 20, 2020

Dense transcript profiling in single cells by image correlation decoding.

Ahmet F Coskun^1,2, Long Cai^1,2

¹Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA.

|June 9, 2016

Summary

This summary is machine-generated.

Correlation FISH (corrFISH) enhances single-cell gene expression analysis by resolving dense barcodes in sequential hybridization. This method accurately quantifies gene expression in cells and tissue, revealing cell-type-specific patterns.

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Last Updated: Mar 19, 2026

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Single-cell Gene Expression Profiling Using FACS and qPCR with Internal Standards

Single-cell Gene Expression Profiling Using FACS and qPCR with Internal Standards

Published on: February 25, 2017

Area of Science:

Molecular Biology
Genomics
Cell Biology

Background:

Sequential barcoded fluorescent in situ hybridization (seqFISH) enables multiplexed detection of molecular species in single cells.
The density of barcoded objects limits multiplexing capabilities in seqFISH.
Accurate quantification of gene expression in situ is crucial for understanding cellular function.

Purpose of the Study:

To develop a novel method, correlation FISH (corrFISH), for resolving dense temporal barcodes in sequential hybridization.
To improve the multiplexing capacity of in situ hybridization techniques.
To investigate cell-type-specific gene expression patterns of highly expressed ribosomal protein genes.

Main Methods:

Development of correlation FISH (corrFISH) to resolve dense temporal barcodes.
Application of corrFISH for quantitative analysis of gene expression in single cultured cells.
Utilizing corrFISH on mouse thymus sections to analyze gene expression in tissue.

Main Results:

corrFISH successfully resolves dense temporal barcodes in sequential hybridization experiments.
The method enabled accurate quantification of highly expressed ribosomal protein genes in single cells.
Cell-type-specific gene expression patterns were revealed in both cultured cells and mouse thymus sections.

Conclusions:

corrFISH significantly advances the capability of in situ hybridization for high-plex molecular detection.
The method provides a powerful tool for dissecting cell-type-specific gene expression.
corrFISH opens new avenues for high-resolution spatial transcriptomics and cell biology research.