The Expression Analysis core offers several services that can be integrated into your Chromatin Immunoprecipitation (ChIP) and chromatin immunoprecipitation-microarray (ChIP-chip) experiments.  These services include the following:

Chromatin Immunoprecipitation Service:  You provide us with cross linked cells, an antibody to a transcription factor or DNA modification, and, if possible, reagents to PCR amplify a target gene.  We will carry out the chromatin immunoprecipitation protocol including sonication optimization, precipitation with your antibody, positive and negative control antibodies, and analysis and quantification of enrichment through target promoter PCR amplification.  Details of how the project would be set up and relevant caveats are explained in this document.

Whole Genome Amplification:  Common method used to amplify low amounts of primary ChIP material to sufficient quantities for dye labeling prior to array hybridization.  Details of utilizing this procedure are found here.

Basic Peak Finding Bioinformatics:  If using Nimblegen arrays, we offer basic instruction in the manufacturer's software packages for peak finding and analysis (NimbleScan 2.3 and Signal Map 1.8).  These programs are available on facility workstations.  We also can provide initial training in peak finding programs developed in the Farnham laboratory.  These programs are written in perl script and can be freely distributed with appropriate accreditation.  Additional support may become available through the bioinformatics core.

Training:  The chromatin immunoprecipitation workshop offered periodically through our core is a great opportunity to familiarize yourself with this technique.  Check out the web site for information on when the next workshop is happening, and also for numerous additional ChIP and ChIP-chip resources.

Chromatin Immunoprecipitation Resources

A good resource for information about primary antibodies that have been shown to work in chromatin immunoprecipitation is the chIP on chip.org site hosted by Bing Ren's lab at UCSD.  Researchers can scan a number of commercial antibodies to see if they've been deemed chIP-worthy.  The site is a little out of date but it still has some useful information.

You might also be interested in looking over a few papers that provide background on the ChIP-chip procedure and illustrate some applications of the technology.

High Throughput Screening of Chromatin Immunoprecipitates Using CpG-Island Microarrays Methods in Enzymology article explaining the basic protocol.  While technical developments have advanced, this paper provides useful background information and rationales for the procedures used.

Use of Chromatin Immunoprecipitation to Clone Novel E2F Target Promoters Primary publication using a protocol very similar to the one used in the workshop.

Locating Mammalian Transcription Factor Binding Sites: A Survey of Computational and Experimental Techniques Recent review outlining the application of ChIP-chip plus in silico techniques for genome wide sequence element characterizations.

Chromatin Immunoprecipitation and Microarray-Based Analysis of Protein Location  Recent techniques oriented paper from another group describing entire ChIP-chip procedure, with detailed protocols and helpful troubleshooting information.

Two-step Cross-linking Method for Identification of NF-kB Gene Network by Chromatin Immunoprecipitation  Demonstration and theoretical discussions on the use of additional cross linkers besides formaldehyde in order to expand information obtained in the ChIP assay.

In vivo Dual Cross-linking for Identification of Indirect DNA-associated Proteins by Chromatin Immunoprecipitation Similar to above paper, explores crosslinkers with different spacer lengths to identify additional proteins in transcription complexes.

Comparison of Sample Preparation Methods for ChIP-chip Assays Recent collaborative effort from the Farnham group and core facility on the use of whole genome amplification (WGA) reagents for ChIP sample amplification.

WGA Publication Supplemental Information Protocols accompanying above paper, includes comprehensive ChIP protocol and WGA protocol.

Whole Genome Amplification Protocol WGA protocol alone, update March 27, 2007.

Chromatin Immunoprecipitation Protocol Latest version of the ChIP protocol, updated July 2nd, 2007.

Workshop Chromatin Immunoprecipitation Protocol Nearly identical to the above protocol, more configured towards workshop specific manipulations.

Chromatin Immunoprecipitation Supplies Vendor and order information for the supplies we use for ChIP experiments.

Farnham Lab Web Site Follow the links from this page to more protocols for ChIP and ChIP-chip, primary publications utilizing these techniques, software analysis tools, and links to numerous other related resources.

Epigenome Network Web Site.  European Union based web site containing solicited protocols from international experts in the fields of ChIP, ChIP-chip, and other epigentic analytical techniques. Our WGA protocol is on this site.

Micro-ChIP protocol.  Protocol developed in Farnham lab for performing ChIP on very small cell numbers, as few as 10,000 cells.