ChIP on Chip

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ChIP-Chip (Chromatin IP on Chip, also called Genome Wide Location Analysis) is a method for studying the regulation of gene expression on a genome-wide scale. Using microarrays that tile either the entire genome, or specific regions of interest like promoters, at high resolution, the interaction of transcriptional regulators and their genes of interest can be studied in detail. This powerful technique can be used to map cell growth, cell cycle, nutrient utilization, stress responses and development. Such insight can be crucial to developing therapeutics to treat disease.

ChIP-Chip service includes Invitrogen Bioprime labeling of amplified genomic DNA, hybridization, washing and scanning of arrays, as well as data extraction.

Please see below for further details about the service.

Sample Submission Guidelines

Customers are urged to provide material which has been amplified by either by LM-PCR or by Sigma’s “GenomePlex-Whole Genome Amplification” protocol in their own laboratories. We will do the Bio-prime labeling before hybridizing to the arrays.


The Whitehead Institute Genome Technology Core primarily uses the Agilent ChIP-Chip platform. A complete description of Agilent’s ChIP-Chip platform, including arrays, reagents and protocols, can be found here:

The WIGTC can also process samples on the Nimblegen and Affymetrix platforms.

Most arrays can be ordered for customers by us. Some minimum orders may apply. Please make sure you specify which array types you would like on your sample submission form.

External customers must order their own Affymetrix arrays and have them drop shipped to us. Please contact us for information.


The following link contains detailed protocols for all steps in ChIP-chip sample preparation. Nature protocols paper

An alternative protocol for amplification of immunoprecipitated DNA is the Sigma GenomePlex -Whole Genome Amplification kit. Details can be found here:


  • Microarray images are scanned for a balanced view and saved in TIFF formats.
  • Numerical intensities are extracted for each probes
  • The results are organized which includes TIFF image files and intensity data files, which is made available to the customer in a CD.

Data in spreadsheet form, along with raw images, will be packaged and delivered either on DVD and/or by FTP. For further information on analysis please contact Sumeet Gupta.