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Related Experiment Video

Updated: Jun 12, 2025

Metabolic Labeling of Newly Transcribed RNA for High Resolution Gene Expression Profiling of RNA Synthesis, Processing and Decay in Cell Culture

Metabolic Labeling of Newly Transcribed RNA for High Resolution Gene Expression Profiling of RNA Synthesis, Processing and Decay in Cell Culture

Published on: August 8, 2013

A protocol for time-resolved transcriptomics through metabolic labeling and combinatorial indexing.

Rory J Maizels¹, Daniel M Snell², James Briscoe²

¹The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; University College London, London, UK.

|October 2, 2024

Summary

This summary is machine-generated.

This study introduces an optimized protocol for metabolic labeling of RNA using 4-thiouridine (4sU) combined with single-cell RNA sequencing. This method enhances the study of gene expression dynamics at the single-cell level.

Keywords:

Cell culture Developmental biology Gene Expression Molecular Biology Molecular/Chemical Probes RNAseq Single Cell

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Last Updated: Jun 12, 2025

Metabolic Labeling of Newly Transcribed RNA for High Resolution Gene Expression Profiling of RNA Synthesis, Processing and Decay in Cell Culture

Metabolic Labeling of Newly Transcribed RNA for High Resolution Gene Expression Profiling of RNA Synthesis, Processing and Decay in Cell Culture

Published on: August 8, 2013

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Published on: March 7, 2018

Extremely Rapid and Specific Metabolic Labelling of RNA In Vivo with 4-Thiouracil Ers4tU

Extremely Rapid and Specific Metabolic Labelling of RNA In Vivo with 4-Thiouracil Ers4tU

Published on: August 22, 2019

Area of Science:

Molecular Biology
Genomics
Biotechnology

Background:

Single-cell transcriptomics offers a snapshot of gene expression but struggles to capture dynamic changes.
Metabolic labeling with 4-thiouridine (4sU) enables temporal RNA profiling at the single-cell level.
Existing protocols may lack optimization for automation and integration with single-cell RNA sequencing.

Purpose of the Study:

To present an optimized and automation-friendly protocol for metabolic RNA labeling coupled with single-cell RNA sequencing.
To enable the study of gene expression dynamics in individual cells.
To provide a robust method for capturing temporal information in RNA expression.

Main Methods:

Optimization of 4-thiouridine (4sU) metabolic labeling for nascent RNA.
Development of cell fixation and chemical treatment procedures compatible with labeling.
Implementation of automated two-level combinatorial indexing for single-cell RNA sequencing.
Integration of metabolic labeling with single-cell RNA sequencing workflow.

Main Results:

An optimized protocol for 4sU metabolic labeling and single-cell RNA sequencing is described.
The protocol is designed to be automation-friendly, facilitating high-throughput applications.
The method allows for the capture of temporal gene expression dynamics at the single-cell level.

Conclusions:

The presented protocol offers a powerful tool for investigating dynamic gene expression in single cells.
This approach overcomes limitations of static transcriptomic snapshots.
The automation-friendly design promotes broader accessibility and application in biological research.