5C Analysis of 3C, ChIP-Loop, and Control Libraries
Department of Biochemistry and Molecular Pharmacology; Program in Systems Biology
Biochemistry | Genetic Phenomena | Genetics and Genomics | Laboratory and Basic Science Research | Molecular Biology | Systems Biology
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
Cold Spring Harb Protoc. 2018 Sep 4;2018(9):pdb.prot097899. doi: 10.1101/pdb.prot097899. Link to article on publisher's site
Cold Spring Harbor protocols
Kim TH, Dekker J. (2018). 5C Analysis of 3C, ChIP-Loop, and Control Libraries. Program in Systems Biology Publications and Presentations. https://doi.org/10.1101/pdb.prot097899. Retrieved from https://escholarship.umassmed.edu/sysbio_pubs/148