Also visit: ChIP Method and Troubleshooting Forum
Summary: Chromatin immunoprecipitation (ChIP) is a powerful tool for identifying proteins, including histone proteins and non-histone proteins, associated with specific regions of the genome by using specific antibodies that recognize a specific protein or a specific modification of a protein. The initial step of ChIP is the cross-linking of protein-protein and protein-DNA in live cells with formaldehyde. After cross-linking, the cells are lysed and crude extracts are sonicated to shear the DNA. Proteins together with cross-linked DNA are subsequently immunoprecipitated. Protein-DNA cross-links in the immunoprecipitated material are then reversed and the DNA fragments are purified and PCR amplified. There are two general types of ChIP experiments: Cross-linking ChIP (X-ChIP or XChIP) which uses chromatin fixed with formaldehyde and fragmented by sonication and native chromatin ChIP (N-ChIP or NChIP) which uses native chromatin prepared by nuclease digestion of cell nuclei.
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Protocols
- ChIP Assay (Farnham Laboratory, UC Davis)
This protocol has successfully used with NIH 3T3, Friend, HeLa, Raji and CHO cells. However, you may have to optimize conditions for your specific cell type.
http://genomics.ucdavis.edu/farnham/pdf/FarnhamLab...
Added: Mon Mar 29 2004, Hits: 9446, Reviews: 0 Write review - Chromatin Immunoprecipitation (ChIP) Assay (Epigenome Network of Excellence)
There is a general protocol for ChIP, which is employed by many different labs with minor modifications. Here described is a modified ChIP protocols used successfully in the athor's lab. They include the Standard Protocol, Re-ChIP, Alternative Crosslinking Method and Nucleosome ChIPs.
http://www.epigenome-noe.net/researchtools/protoco...
Added: Mon Feb 09 2009, Hits: 3834, Reviews: 0 Write review Cached - Chromatin Immunoprecipitation (ChIP) Assay Protocol
(Genome Center, UC Davis)
Standard and verified ChIP protocol
http://www.genomecenter.ucdavis.edu/expression_ana...
Added: Tue Jan 27 2009, Hits: 9820, Reviews: 0 Write review - Chromatin Immunoprecipitation from Human Embryonic Stem Cells
(Journal of Visualized Experiments)
Chromatin immunoprecipitation involves the purification of in vivo cross-linked chromatin. The isolated chromatin is reduced to smaller fragments by enzymatic digestion or mechanical force. Chromatin fragments are precipitated using specific antibodies to target proteins or protein and DNA modifications. The precipitated DNA or RNA is purified and used as a template for PCR or DNA microarray based assays.
http://www.jove.com/index/details.stp?ID=780
Added: Mon Feb 09 2009, Hits: 3085, Reviews: 0 Write review Cached - Formaldehyde Crosslinking and ChIP Assay (Mirmira Laboratory at the University of Virginia)
If you want to start a ChIP experiment without buying a kit, here is the protocol to follow. It guides you through a 50-step protocol from formaldehyde crosslinking to ChIP and also provides receipes for all home-made reagents.
http://faculty.virginia.edu/mirmira/resources_file...
Added: Sat Jun 05 2004, Hits: 5105, Reviews: 0 Write review Cached -
Carrier ChIP (CChIP) Protocol
(Epigenome Network of Excellence)
CChIP, based on the use of carrier chromatin, allows detailed and reproducible epigenetic analysis of as few as 100 cells. The procedure has been validated with primary mouse embryo material, but should be applicable to cells from various sources, including tissue biopsies and FACS-sorted cell populations. The protocol is for analysis of histone modifications in native, unfixed chromatin prepared by micrococcal nuclease digestion.
http://www.epigenome-noe.net/researchtools/protoco...
Added: Tue Jan 27 2009, Hits: 956, Reviews: 0 Write review Cached -
ChIP Assay
(The Morimoto Lab, Northwestern University)
http://www.biochem.northwestern.edu/morimoto/resea...
Added: Mon Mar 29 2004, Hits: 4641, Reviews: 0 Write review -
ChIP assay
(Breeden Lab, Fred Hutchinson Cancer Research Center)
The ChIP assay is the key biochemical method used to map the location of modified histones and other chromosomal proteins in the genome. The important feature of these experiments is the use of an antibody that recognises and binds to the protein of interest, not only in free solution, but also when assembled into chromatin. ChIP assay combines two straightforward steps — first, in vivo formaldehyde cross-linking of whole cells that freezes protein-protein and protein-DNA interactions, followed by immunoprecipitation of protein-DNA complexes with specific antibodies from sonicated extracts.
http://labs.fhcrc.org/breeden/Methods/yeast%20meth...
Added: Wed Feb 19 2003, Hits: 4804, Reviews: 0 Write review Cached -
ChIP assay
(Jeffrey M. Rosen, Department of Molecular and Cellular Biology, Baylor College of Medicine)
Formaldehyde cross-linking and chromatin immunoprecipitation assays of tissueculture cells are performed as described by Boyd and Farnham (MCB 29:8389-8399) andY. Shang et. al. (Cell 103:843-852) with some modifications
http://public.bcm.tmc.edu/rosenlab/protocols/ChIP....
Added: Wed Feb 19 2003, Hits: 4404, Reviews: 0 Write review -
ChIP Assay
(Bissell Lab, Berkely Lab)
A protocol based on upstate ChIP protocol
http://www.lbl.gov/LBL-Programs/lifesciences/Bisse...
Added: Sat Feb 21 2009, Hits: 4193, Reviews: 0 Write review Cached -
ChIP Troubleshootings
(Protocol Online)
Archives of hundreds or threads of ChIP troubleshootings
http://www.protocol-online.org/biology-forums/ChIP...
Added: Wed Feb 11 2009, Hits: 3265, Reviews: 0 Write review Cached -
ChIP-CpG Island Microarray Binding Analysis
(Farnham Laboratory, UC Davis)
Adaptation of the chromatin immunoprecipitation (ChIP) assay to a high-throughput microarray based method for discovering genomic regions occupied by human DNA-binding proteins.
http://genomics.ucdavis.edu/farnham/protocols/MOJO...
Added: Mon Mar 29 2004, Hits: 3551, Reviews: 0 Write review -
ChIPs Cloning
(Farnham Laboratory, UC Davis)
Combines ChIP assay with subsequent DNA cloning.
http://genomics.ucdavis.edu/farnham/protocols/ChIP...
Added: Mon Mar 29 2004, Hits: 1709, Reviews: 0 Write review Cached -
Chromatin Immunoprecipitation (ChIPs) Cloning Protocol
(Farnham Laboratory, UC Davis)
Cloning pulled down DNA from ChIP assay
http://genomics.ucdavis.edu/farnham/protocols/ChIP...
Added: Sat Jan 31 2009, Hits: 1949, Reviews: 0 Write review Cached -
Chromatin Immunoprecipitation Protocol for Histone Modification & Chromatin Associated Proteins
(Epigenome Network of Excellence)
This protocol has been successfully used in experiments with Mouse Embryonic Stem (ES) cells, Embryonic Fibroblasts (MEF), Trophoblast Stem (TS) cells, B-lymphocytes and hepatocytes, as well as with U2OS, 293, Hela, T98G cells from human.
http://www.epigenome-noe.net/researchtools/protoco...
Added: Mon Feb 09 2009, Hits: 1154, Reviews: 0 Write review Cached - Rapid Chromatin De-crosslinking (Protocol Online)
For checking how well one's chromatin is sonicated, this is a fast (2 hour total) alternative to standard methods and yields nearly identical results.
Added: Tue Aug 16 2011, Reviews: 0 Write review
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