Title

5C Analysis of 3C, ChIP-Loop, and Control Libraries

UMMS Affiliation

Department of Biochemistry and Molecular Pharmacology; Program in Systems Biology

Publication Date

2018-09-04

Document Type

Article

Disciplines

Biochemistry | Genetic Phenomena | Genetics and Genomics | Laboratory and Basic Science Research | Molecular Biology | Systems Biology

Abstract

This protocol describes the 5C method of detecting ligation products in 3C, ChIP-loop, or control libraries. The method starts with a purified 3C library, a purified ChIP-loop library, or a purified control library. Before starting the protocol, assess the quality of the library that will be used by performing semiquantitative polymerase chain reaction (PCR). Ligation products should be readily detectable and nearby restriction fragments should be ligated more frequently than distant fragments. The design of the 5C primers and methods to determine interaction frequencies are also described in this protocol.

DOI of Published Version

10.1101/pdb.prot097899

Source

Cold Spring Harb Protoc. 2018 Sep 4;2018(9):pdb.prot097899. doi: 10.1101/pdb.prot097899. Link to article on publisher's site

Journal/Book/Conference Title

Cold Spring Harbor protocols

Related Resources

Link to Article in PubMed

PubMed ID

30181223

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