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Updated: May 7, 2026

Transcriptome Analysis of Single Cells

Transcriptome Analysis of Single Cells

Published on: April 25, 2011

Image-based transcriptomics in thousands of single human cells at single-molecule resolution.

Nico Battich¹, Thomas Stoeger, Lucas Pelkmans

¹1] Faculty of Sciences, Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland. [2] Systems Biology PhD program, Life Science Zurich Graduate School, ETH Zurich and University of Zurich, Zurich, Switzerland. [3].

|October 8, 2013

Summary

New branched DNA technology enables scalable, single-molecule resolution quantification of transcript abundance and spatial properties in thousands of single cells. This method allows unbiased identification of in situ transcriptome signatures for functional interpretation of gene expression variability.

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Area of Science:

Molecular Biology
Cell Biology
Genomics

Background:

Fluorescence in situ hybridization (FISH) is a key technique for analyzing transcript copy number and subcellular localization in single cells.
Current FISH methods face limitations in scalability for whole-transcriptome analysis.

Purpose of the Study:

To develop a scalable method for high-resolution transcriptomic analysis in single cells.
To enable quantitative analysis of transcript abundance and spatial distribution across thousands of cells.

Main Methods:

Integration of branched DNA technology with automated liquid handling.
Application of high-content imaging and quantitative image analysis.
Single-molecule resolution for transcript quantification.

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Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

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Published on: January 10, 2019

A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations

A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations

Published on: October 25, 2018

Related Experiment Videos

Last Updated: May 7, 2026

Transcriptome Analysis of Single Cells

Transcriptome Analysis of Single Cells

Published on: April 25, 2011

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations

A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations

Published on: October 25, 2018

Main Results:

Highly reproducible quantification of transcript abundance in thousands of single cells.
Extraction of multivariate features detailing transcript subcellular patterning and spatial properties.
Characterization of cell-to-cell variability in transcript distribution.

Conclusions:

The developed method allows unbiased identification of in situ transcriptome signatures without perturbations.
Enables functional interpretation of cell-to-cell variability in gene expression.
Broad applicability in various high-throughput image-based approaches is expected.