دورية أكاديمية
Calculating RNA degradation rates using large-scale normalization in mouse embryonic stem cells.
| العنوان: | Calculating RNA degradation rates using large-scale normalization in mouse embryonic stem cells. |
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| المؤلفون: | Viegas JO; Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel., Fishman L; Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel., Meshorer E; Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel; The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel. Electronic address: eran.meshorer@mail.huji.ac.il., Rabani M; Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel. Electronic address: michal.rabani@mail.huji.ac.il. |
| المصدر: | STAR protocols [STAR Protoc] 2023 Sep 15; Vol. 4 (3), pp. 102534. Date of Electronic Publication: 2023 Sep 05. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Cell Press Country of Publication: United States NLM ID: 101769501 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2666-1667 (Electronic) Linking ISSN: 26661667 NLM ISO Abbreviation: STAR Protoc Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: [Cambridge, MA] : Cell Press, [2020]- |
| مواضيع طبية MeSH: | Mouse Embryonic Stem Cells* , Alpha-Amanitin*/pharmacology, Animals ; Mice ; Genomics ; RNA/genetics ; RNA-Seq |
| مستخلص: | 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 . Competing Interests: Declaration of interests The authors declare no competing interests. (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.) |
| فهرسة مساهمة: | Keywords: Cell Biology; Cell Differentiation; Molecular Biology; RNA-seq; Stem Cells |
| المشرفين على المادة: | 0 (Alpha-Amanitin) 63231-63-0 (RNA) |
| تواريخ الأحداث: | Date Created: 20230901 Date Completed: 20240308 Latest Revision: 20240308 |
| رمز التحديث: | 20240308 |
| مُعرف محوري في PubMed: | PMC10495639 |
| DOI: | 10.1016/j.xpro.2023.102534 |
| PMID: | 37656628 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 2666-1667 |
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| DOI: | 10.1016/j.xpro.2023.102534 |