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An optimized 4C-seq protocol based on cistrome and epigenome data in the mouse RAW264.7 macrophage cell line

Chromosome conformation capture combined with high-throughput sequencing (4C-seq) is a powerful tool to map genomic DNA regions that communicate with a specific locus of interest such as functional single-nucleotide polymorphism (SNPs)-containing regions. This protocol describes detailed steps to pe...

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Detalles Bibliográficos
Autores principales: Huang, Zhiqiang, Wang, Cheng, Treuter, Eckardt, Fan, Rongrong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9043770/
https://www.ncbi.nlm.nih.gov/pubmed/35496794
http://dx.doi.org/10.1016/j.xpro.2022.101338
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author Huang, Zhiqiang
Wang, Cheng
Treuter, Eckardt
Fan, Rongrong
author_facet Huang, Zhiqiang
Wang, Cheng
Treuter, Eckardt
Fan, Rongrong
author_sort Huang, Zhiqiang
collection PubMed
description Chromosome conformation capture combined with high-throughput sequencing (4C-seq) is a powerful tool to map genomic DNA regions that communicate with a specific locus of interest such as functional single-nucleotide polymorphism (SNPs)-containing regions. This protocol describes detailed steps to perform 4C-seq in mouse macrophage RAW264.7 cells, starting from the primer design based on cistrome and epigenome data, sample processing, and to the bioinformatics analysis. For complete details on the use and execution of this protocol, please refer to Huang et al. (2021).
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spelling pubmed-90437702022-04-28 An optimized 4C-seq protocol based on cistrome and epigenome data in the mouse RAW264.7 macrophage cell line Huang, Zhiqiang Wang, Cheng Treuter, Eckardt Fan, Rongrong STAR Protoc Protocol Chromosome conformation capture combined with high-throughput sequencing (4C-seq) is a powerful tool to map genomic DNA regions that communicate with a specific locus of interest such as functional single-nucleotide polymorphism (SNPs)-containing regions. This protocol describes detailed steps to perform 4C-seq in mouse macrophage RAW264.7 cells, starting from the primer design based on cistrome and epigenome data, sample processing, and to the bioinformatics analysis. For complete details on the use and execution of this protocol, please refer to Huang et al. (2021). Elsevier 2022-04-19 /pmc/articles/PMC9043770/ /pubmed/35496794 http://dx.doi.org/10.1016/j.xpro.2022.101338 Text en © 2022 The Author(s) https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Protocol
Huang, Zhiqiang
Wang, Cheng
Treuter, Eckardt
Fan, Rongrong
An optimized 4C-seq protocol based on cistrome and epigenome data in the mouse RAW264.7 macrophage cell line
title An optimized 4C-seq protocol based on cistrome and epigenome data in the mouse RAW264.7 macrophage cell line
title_full An optimized 4C-seq protocol based on cistrome and epigenome data in the mouse RAW264.7 macrophage cell line
title_fullStr An optimized 4C-seq protocol based on cistrome and epigenome data in the mouse RAW264.7 macrophage cell line
title_full_unstemmed An optimized 4C-seq protocol based on cistrome and epigenome data in the mouse RAW264.7 macrophage cell line
title_short An optimized 4C-seq protocol based on cistrome and epigenome data in the mouse RAW264.7 macrophage cell line
title_sort optimized 4c-seq protocol based on cistrome and epigenome data in the mouse raw264.7 macrophage cell line
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9043770/
https://www.ncbi.nlm.nih.gov/pubmed/35496794
http://dx.doi.org/10.1016/j.xpro.2022.101338
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