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Updated: Feb 25, 2026

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

Simultaneous epitope and transcriptome measurement in single cells.

Marlon Stoeckius¹, Christoph Hafemeister¹, William Stephenson¹

¹New York Genome Center, New York, New York, USA.

|August 1, 2017

Summary

This summary is machine-generated.

Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) integrates cell surface protein data with single-cell RNA sequencing. This method enhances understanding of complex cellular populations by providing both transcriptome and proteome information.

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Last Updated: Feb 25, 2026

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

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Isolation of Adipose Tissue Nuclei for Single-Cell Genomic Applications

Isolation of Adipose Tissue Nuclei for Single-Cell Genomic Applications

Published on: June 12, 2020

Area of Science:

Molecular Biology
Genomics
Immunology

Background:

High-throughput single-cell RNA sequencing (scRNA-seq) is crucial for analyzing cellular heterogeneity.
scRNA-seq lacks the ability to measure cell surface protein expression, limiting phenotypic characterization.
Understanding cell surface markers is vital for defining cell states and functions.

Purpose of the Study:

To develop a novel method integrating transcriptome and proteome profiling at the single-cell level.
To provide a comprehensive single-cell analysis solution combining gene expression and cell surface protein data.
To overcome the limitations of existing single-cell sequencing techniques.

Main Methods:

Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) utilizes oligonucleotide-labeled antibodies.
Antibodies target specific cell surface proteins, with their attached oligonucleotides serving as unique barcodes.
These barcodes are detected alongside mRNA transcripts during high-throughput sequencing.

Main Results:

CITE-seq successfully integrates single-cell RNA sequencing with cell surface protein measurements.
The method provides a high-resolution, multi-modal readout of cellular identity.
Demonstrated compatibility with established single-cell sequencing workflows.

Conclusions:

CITE-seq offers an efficient and scalable approach for simultaneous transcriptome and proteome analysis in single cells.
This technique significantly advances the study of complex biological systems by providing deeper cellular insights.
CITE-seq empowers researchers to dissect cellular heterogeneity with unprecedented detail.