Calculating RNA degradation rates using large-scale normalization in mouse embryonic stem cells

Juliane Oliveira Viegas, Lior Fishman, Eran Meshorer*, Michal Rabani*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Data normalization is critical to the process of estimating RNA degradation by analyzing RNA levels when transcription is blocked. Here, we present a protocol for measuring mRNA degradation rates, optimized for mouse embryonic stem cells, using α-amanitin inhibitor. We describe steps for a time course α-amanitin treatment, RNA-seq, and alignment; we then detail procedures for analyzing data and sequence enrichment. Our method relies on large-scale normalization of stable transcripts in genomic RNA-seq measurements, providing reliable readouts. For complete details on the use and execution of this protocol, please refer to Viegas et al.1

Original languageAmerican English
Article number102534
JournalSTAR Protocols
Issue number3
StatePublished - 15 Sep 2023

Bibliographical note

Funding Information:
This work was supported by the Israel Ministry of Science ( MOST 0004272 to E.M.), the European Innovation Council (EIC) Horizon Europe ( RT-SuperES 101099654 to E.M.), and the European Research Council (ERC) Horizon 2020 grant ( 852451 to M.R.). E.M. is the incumbent of the Arthur Gutterman Professor Chair for Stem Cell Research. J.V. is supported by the European Union’s Horizon -2020 Marie Skłodowska Curie EpiSyStem ITN Network ( 765966 ).

Publisher Copyright:
© 2023 The Authors


  • Cell Biology
  • Cell Differentiation
  • Molecular Biology
  • RNA-seq
  • Stem Cells


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