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End-to-end pipeline for differential analysis of pausing in ribosome profiling data

Ribosome profiling is a powerful technique which maps the distribution of ribosomes along mRNAs to analyze translation genome-wide. Ribosome density can be affected by multiple factors, such as changes to translation initiation or elongation rates. We describe the application of a metric for identif...

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Detalles Bibliográficos
Autores principales: Flanagan, Keegan, Li, Wanxin, Greenblatt, Ethan J., Dao Duc, Khanh
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9405084/
https://www.ncbi.nlm.nih.gov/pubmed/36035799
http://dx.doi.org/10.1016/j.xpro.2022.101605
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author Flanagan, Keegan
Li, Wanxin
Greenblatt, Ethan J.
Dao Duc, Khanh
author_facet Flanagan, Keegan
Li, Wanxin
Greenblatt, Ethan J.
Dao Duc, Khanh
author_sort Flanagan, Keegan
collection PubMed
description Ribosome profiling is a powerful technique which maps the distribution of ribosomes along mRNAs to analyze translation genome-wide. Ribosome density can be affected by multiple factors, such as changes to translation initiation or elongation rates. We describe the application of a metric for identifying genes rate-limited by these rates by analyzing the relative distribution of ribosome footprints along transcripts. This protocol also details two sample analyses comparing gene translation efficiencies and the distribution of ribosome densities on downloadable datasets. For complete details on the use and execution of this protocol, please refer to Flanagan et al. (2022).
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spelling pubmed-94050842022-08-26 End-to-end pipeline for differential analysis of pausing in ribosome profiling data Flanagan, Keegan Li, Wanxin Greenblatt, Ethan J. Dao Duc, Khanh STAR Protoc Protocol Ribosome profiling is a powerful technique which maps the distribution of ribosomes along mRNAs to analyze translation genome-wide. Ribosome density can be affected by multiple factors, such as changes to translation initiation or elongation rates. We describe the application of a metric for identifying genes rate-limited by these rates by analyzing the relative distribution of ribosome footprints along transcripts. This protocol also details two sample analyses comparing gene translation efficiencies and the distribution of ribosome densities on downloadable datasets. For complete details on the use and execution of this protocol, please refer to Flanagan et al. (2022). Elsevier 2022-08-18 /pmc/articles/PMC9405084/ /pubmed/36035799 http://dx.doi.org/10.1016/j.xpro.2022.101605 Text en © 2022 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
Flanagan, Keegan
Li, Wanxin
Greenblatt, Ethan J.
Dao Duc, Khanh
End-to-end pipeline for differential analysis of pausing in ribosome profiling data
title End-to-end pipeline for differential analysis of pausing in ribosome profiling data
title_full End-to-end pipeline for differential analysis of pausing in ribosome profiling data
title_fullStr End-to-end pipeline for differential analysis of pausing in ribosome profiling data
title_full_unstemmed End-to-end pipeline for differential analysis of pausing in ribosome profiling data
title_short End-to-end pipeline for differential analysis of pausing in ribosome profiling data
title_sort end-to-end pipeline for differential analysis of pausing in ribosome profiling data
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9405084/
https://www.ncbi.nlm.nih.gov/pubmed/36035799
http://dx.doi.org/10.1016/j.xpro.2022.101605
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