Program in Systems Biology; Department of Biochemistry and Molecular Pharmacology
Laboratory and Basic Science Research | Molecular Biology | Systems Biology
Owing to its digital nature, ChIP-seq has become the standard method for genome-wide ChIP analysis. Using next-generation sequencing platforms (notably the Illumina Genome Analyzer), millions of short sequence reads can be obtained. The densities of recovered ChIP sequence reads along the genome are used to determine the binding sites of the protein. Although a relatively small amount of ChIP DNA is required for ChIP-seq, the current sequencing platforms still require amplification of the ChIP DNA by ligation-mediated PCR (LM-PCR). This protocol, which involves linker ligation followed by size selection, is the standard ChIP-seq protocol using an Illumina Genome Analyzer. The size-selected ChIP DNA is amplified by LM-PCR and size-selected for the second time. The purified ChIP DNA is then loaded into the Genome Analyzer. The ChIP DNA can also be processed in parallel for ChIP-chip results.
DOI of Published Version
Cold Spring Harb Protoc. 2018 May 1;2018(5):pdb.prot082644. doi: 10.1101/pdb.prot082644. Link to article on publisher's site
Cold Spring Harbor protocols
Kim TH, Dekker J. (2018). ChIP-seq. Program in Systems Biology Publications. https://doi.org/10.1101/pdb.prot082644. Retrieved from https://escholarship.umassmed.edu/sysbio_pubs/128