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

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

STAR protocols (2022-05-03)
Zhiqiang Huang, Cheng Wang, Eckardt Treuter, Rongrong Fan
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).

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
HEPES, ≥99.5% (titration)
Sigma-Aldrich
IL-4 from mouse, Animal-component free, recombinant, expressed in E. coli, ≥98% (SDS-PAGE), ≥98% (HPLC), suitable for cell culture