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Related Experiment Video

Updated: Jul 17, 2025

Determining Genome-wide Transcript Decay Rates in Proliferating and Quiescent Human Fibroblasts
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Calculating RNA degradation rates using large-scale normalization in mouse embryonic stem cells.

Juliane Oliveira Viegas1, Lior Fishman1, Eran Meshorer2

  • 1Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel.

STAR Protocols
|September 1, 2023
PubMed
Summary

This study introduces a new protocol for measuring mRNA degradation rates in mouse embryonic stem cells. The method uses large-scale normalization of stable transcripts for reliable RNA sequencing data analysis.

Keywords:
Cell BiologyCell DifferentiationMolecular BiologyRNA-seqStem Cells

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Accurate measurement of RNA degradation is essential for understanding gene regulation.
  • Existing methods may lack precision or scalability for complex biological systems.

Purpose of the Study:

  • To present a refined protocol for quantifying mRNA degradation rates.
  • To optimize RNA sequencing (RNA-seq) analysis for studying transcript stability.

Main Methods:

  • Utilized a time-course α-amanitin treatment in mouse embryonic stem cells.
  • Performed RNA sequencing (RNA-seq) and subsequent data alignment.
  • Implemented large-scale normalization of stable transcripts for genomic RNA-seq data.

Main Results:

  • Developed a reliable protocol for measuring mRNA degradation rates.
  • The method ensures accurate readouts through robust data normalization techniques.

Conclusions:

  • The presented protocol offers a dependable approach for assessing mRNA decay.
  • This method is optimized for mouse embryonic stem cells and RNA-seq analysis.