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

Zhiqiang Huang; Cheng Wang; Eckardt Treuter; Rongrong Fan

doi:10.1016/j.xpro.2022.101338

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

STAR Protoc. 2022 Apr 19;3(2):101338. doi: 10.1016/j.xpro.2022.101338. eCollection 2022 Jun 17.

Authors

Zhiqiang Huang¹, Cheng Wang², Eckardt Treuter¹, Rongrong Fan¹

Affiliations

¹ Department of Biosciences and Nutrition, Karolinska Institutet, NEO, 14183 Huddinge, Sweden.
² Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.

Abstract

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).

Keywords: Bioinformatics; Cell Biology; Cell culture; Genomics; Molecular Biology; Sequence analysis; Sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Chromosomes
Epigenome*
High-Throughput Nucleotide Sequencing* / methods
Macrophages
Mice
RAW 264.7 Cells