Overview: 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://genomecenter.ucdavis.edu/farnham/farnham/pr...
Added: Mon Mar 29 2004, Hits: 20538, Reviews: 0 Write review Cached - ChIP Assay Protocol (The Epigenome Network of Excellence)
Well-written chromatin immunoprecipitation protocol for histone modification & chromatin associated proteins.
http://www.epigenome-noe.net/researchtools/protoco...
Added: Sat Mar 18 2006, Hits: 4972, Reviews: 0 Write review Cached - ChIP Protocol
(UHN Microarray Center)
Well written and detailed ChIP and microarray protocol.
http://www.microarrays.ca/support/PDFs/ChIP_Protoc...
Added: Thu Jan 27 2005, Hits: 13662, Reviews: 0 Write review - 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: 12403, Reviews: 0 Write review Cached - Standard ChIP Protocol with Modifications (The Epigenome Network of Excellence )
This is a general protocol for ChIP, also includes modifications such as re-ChIP, alternative crosslinking, andnNucleosome ChIPs.
http://www.epigenome-noe.net/researchtools/protoco...
Added: Sat Mar 18 2006, Hits: 3320, Reviews: 0 Write review Cached -
Carrier ChIP (CChIP)
(Epigenome Network of Excellence)
new
Conventional ChIP generally requires a huge number of cells, which limits its applicability. To address this, we have developed a new protocol, CChIP, based on the use of carrier chromatin, that 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 given here is for analysis of histone modifications in native, unfixed chromatin prepared by micrococcal nuclease digestion.
http://www.epigenome-noe.net/researchtools/protoco...
Added: Mon Aug 04 2008, Hits: 1, Reviews: 0 Write review -
ChIP
(OpenWetWare)
Chromatin Immunoprecipitation determines the in vivo chromatin binding sites of a transcription factor or other protein of interest.
http://openwetware.org/wiki/ChIP
Added: Sun Mar 04 2007, Hits: 1566, Reviews: 0 Write review Cached -
ChIP Assay
(The Morimoto Lab, Northwestern University)
http://www.biochem.northwestern.edu/ibis/morimoto/...
Added: Mon Mar 29 2004, Hits: 8368, 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://www.fhcrc.org/labs/breeden/Methods/chromati...
Added: Wed Feb 19 2003, Hits: 10058, 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://www.bcm.edu/rosenlab/protocols/ChIP.pdf
Added: Wed Feb 19 2003, Hits: 7777, Reviews: 0 Write review
Trouble Shootings and FAQs
- ChIp assay on myocytes or tissues?
- Advice on ChIP assay
- Sonication settings for ChIP assay
- How to sonicate DNA in a water bath for ChIP
- ChIP sonication woes- Losing DNA?
- ChIP against transcription factors
- PCR for ChIP not working
- ChIP - Foaming in sonication and other woes
- Is proteinase K digestion necessary and what alternative to sonication for DNA shearing?
- ChIP DNA purification methods
- ChIP - no immunoprecipitated DNA
- MNase vs sonication for ChIP