Abstract
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 language | English |
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Article number | 102534 |
Journal | STAR Protocols |
Volume | 4 |
Issue number | 3 |
DOIs | |
State | Published - 15 Sep 2023 |
Bibliographical note
Publisher Copyright:© 2023 The Authors
Keywords
- Cell Biology
- Cell Differentiation
- Molecular Biology
- RNA-seq
- Stem Cells