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MERR APEX-seq protocol for profiling the subcellular nascent transcriptome in mammalian cells

Knowledge about the spatial organization of RNAs in eukaryotic cells is crucial for understanding their functions. Here, we present a detailed MERR APEX-seq protocol to achieve spatiotemporally resolved mapping of the subcellular transcriptome in cultured mammalian cells. This protocol provides deta...

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Detalles Bibliográficos
Autores principales: Li, Ran, Zou, Peng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9898802/
https://www.ncbi.nlm.nih.gov/pubmed/36853684
http://dx.doi.org/10.1016/j.xpro.2023.102057
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author Li, Ran
Zou, Peng
author_facet Li, Ran
Zou, Peng
author_sort Li, Ran
collection PubMed
description Knowledge about the spatial organization of RNAs in eukaryotic cells is crucial for understanding their functions. Here, we present a detailed MERR APEX-seq protocol to achieve spatiotemporally resolved mapping of the subcellular transcriptome in cultured mammalian cells. This protocol provides detailed description of constructing cell lines stably expressing APEX2, immunofluorescence characterization, MERR APEX labeling, enrichment of biotinylated RNA, library construction and high-throughput sequencing, and MERR APEX-seq data analysis. For complete details on the use and execution of this protocol, please refer to Li et al. (2022).(1)
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spelling pubmed-98988022023-02-05 MERR APEX-seq protocol for profiling the subcellular nascent transcriptome in mammalian cells Li, Ran Zou, Peng STAR Protoc Protocol Knowledge about the spatial organization of RNAs in eukaryotic cells is crucial for understanding their functions. Here, we present a detailed MERR APEX-seq protocol to achieve spatiotemporally resolved mapping of the subcellular transcriptome in cultured mammalian cells. This protocol provides detailed description of constructing cell lines stably expressing APEX2, immunofluorescence characterization, MERR APEX labeling, enrichment of biotinylated RNA, library construction and high-throughput sequencing, and MERR APEX-seq data analysis. For complete details on the use and execution of this protocol, please refer to Li et al. (2022).(1) Elsevier 2023-01-24 /pmc/articles/PMC9898802/ /pubmed/36853684 http://dx.doi.org/10.1016/j.xpro.2023.102057 Text en © 2023 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Protocol
Li, Ran
Zou, Peng
MERR APEX-seq protocol for profiling the subcellular nascent transcriptome in mammalian cells
title MERR APEX-seq protocol for profiling the subcellular nascent transcriptome in mammalian cells
title_full MERR APEX-seq protocol for profiling the subcellular nascent transcriptome in mammalian cells
title_fullStr MERR APEX-seq protocol for profiling the subcellular nascent transcriptome in mammalian cells
title_full_unstemmed MERR APEX-seq protocol for profiling the subcellular nascent transcriptome in mammalian cells
title_short MERR APEX-seq protocol for profiling the subcellular nascent transcriptome in mammalian cells
title_sort merr apex-seq protocol for profiling the subcellular nascent transcriptome in mammalian cells
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9898802/
https://www.ncbi.nlm.nih.gov/pubmed/36853684
http://dx.doi.org/10.1016/j.xpro.2023.102057
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