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Updated: May 27, 2025

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

Linking single-cell transcriptomes with secretion using SEC-seq.

Justin Langerman¹, Sevana Baghdasarian², Rene Yu-Hong Cheng^3,4

¹Department of Biological Chemistry, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA, USA.

Nature Protocols

|February 20, 2025

Summary

This summary is machine-generated.

Scientists developed SEC-seq, a new method linking protein secretion levels to gene expression in single cells. This breakthrough helps understand cell function and engineer better cell therapies by analyzing secreted biomolecules.

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Last Updated: May 27, 2025

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

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Published on: January 10, 2019

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Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

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Published on: January 7, 2020

Area of Science:

Cell Biology
Molecular Biology
Biotechnology

Background:

Cells secrete diverse biomolecules for critical functions like cell communication and pathogen defense.
The therapeutic efficacy of cell therapies relies on the secretion of specific molecules such as cytokines and growth factors.
Understanding the gene expression states that dictate cellular secretion patterns is crucial but largely unknown.

Purpose of the Study:

To develop a novel protocol linking the amount of secreted target proteins to transcriptional sequencing in single cells.
To enable a deeper understanding of the relationship between gene expression and secretory phenotypes.
To facilitate the engineering of improved cell-based therapies.

Main Methods:

Developed SEC-seq (Secretion amount linked to gene expression via Sequencing) utilizing microscale hydrogel particles (Nanovials).
Nanovials capture cells and their secretions, using oligonucleotide-labeled antibodies to tag secretions.
Integrated flow cytometry and single-cell RNA-sequencing (scRNA-seq) for simultaneous analysis of cell transcriptomes and secretion levels.

Main Results:

Successfully linked T cell receptor sequences to cytokine secretion levels.
Identified a highly secreting, potentially regenerative population of mesenchymal stromal cells based on surface marker gene expression.
Correlated transcriptomes with high immunoglobulin secretion in plasma cells.

Conclusions:

SEC-seq provides a versatile method for quantifying protein secretion and linking it to gene expression across various cell types.
The protocol is rapid, with key steps completed in under 4 hours.
SEC-seq offers a generalizable solution for studying cell secretion, advancing our understanding and engineering of cell therapies.