PEM-seq comprehensively quantifies DNA repair outcomes during gene-editing and DSB repair

The repair products of double-stranded DNA breaks (DSBs) are crucial for investigating the mechanism underlying DNA damage repair as well as evaluating the safety and efficiency of gene-editing; however, a comprehensively quantitative assay remains to be established. Here, we describe the step-by-st...

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Autores principales: Liu, Yang, Yin, Jianhang, Gan, Tingting, Liu, Mengzhu, Xin, Changchang, Zhang, Weiwei, Hu, Jiazhi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9019705/
https://www.ncbi.nlm.nih.gov/pubmed/35462794
http://dx.doi.org/10.1016/j.xpro.2021.101088
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author Liu, Yang
Yin, Jianhang
Gan, Tingting
Liu, Mengzhu
Xin, Changchang
Zhang, Weiwei
Hu, Jiazhi
author_facet Liu, Yang
Yin, Jianhang
Gan, Tingting
Liu, Mengzhu
Xin, Changchang
Zhang, Weiwei
Hu, Jiazhi
author_sort Liu, Yang
collection PubMed
description The repair products of double-stranded DNA breaks (DSBs) are crucial for investigating the mechanism underlying DNA damage repair as well as evaluating the safety and efficiency of gene-editing; however, a comprehensively quantitative assay remains to be established. Here, we describe the step-by-step instructions of the primer extension-mediated sequencing (PEM-seq), followed by the framework of data processing and statistical analysis. PEM-seq presents a full spectrum of repair outcomes for both genome-editing-induced and endogenous DSBs in mouse and human cells. For complete details on the use and execution of this profile, please refer to Gan et al. (2021), Yin et al. (2019), Liu et al. (2021a), and Zhang et al. (2021).
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spelling pubmed-90197052022-04-21 PEM-seq comprehensively quantifies DNA repair outcomes during gene-editing and DSB repair Liu, Yang Yin, Jianhang Gan, Tingting Liu, Mengzhu Xin, Changchang Zhang, Weiwei Hu, Jiazhi STAR Protoc Protocol The repair products of double-stranded DNA breaks (DSBs) are crucial for investigating the mechanism underlying DNA damage repair as well as evaluating the safety and efficiency of gene-editing; however, a comprehensively quantitative assay remains to be established. Here, we describe the step-by-step instructions of the primer extension-mediated sequencing (PEM-seq), followed by the framework of data processing and statistical analysis. PEM-seq presents a full spectrum of repair outcomes for both genome-editing-induced and endogenous DSBs in mouse and human cells. For complete details on the use and execution of this profile, please refer to Gan et al. (2021), Yin et al. (2019), Liu et al. (2021a), and Zhang et al. (2021). Elsevier 2022-01-17 /pmc/articles/PMC9019705/ /pubmed/35462794 http://dx.doi.org/10.1016/j.xpro.2021.101088 Text en © 2021 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
Liu, Yang
Yin, Jianhang
Gan, Tingting
Liu, Mengzhu
Xin, Changchang
Zhang, Weiwei
Hu, Jiazhi
PEM-seq comprehensively quantifies DNA repair outcomes during gene-editing and DSB repair
title PEM-seq comprehensively quantifies DNA repair outcomes during gene-editing and DSB repair
title_full PEM-seq comprehensively quantifies DNA repair outcomes during gene-editing and DSB repair
title_fullStr PEM-seq comprehensively quantifies DNA repair outcomes during gene-editing and DSB repair
title_full_unstemmed PEM-seq comprehensively quantifies DNA repair outcomes during gene-editing and DSB repair
title_short PEM-seq comprehensively quantifies DNA repair outcomes during gene-editing and DSB repair
title_sort pem-seq comprehensively quantifies dna repair outcomes during gene-editing and dsb repair
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9019705/
https://www.ncbi.nlm.nih.gov/pubmed/35462794
http://dx.doi.org/10.1016/j.xpro.2021.101088
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