Top : Molecular Biology : Protein : Immunoprecipitation (IP) : Chromatin Immunoprecipitation (ChIP Assay) : ChIP on Chip

Summary: ChIP-on-chip (chromatin immunoprecipitation-on-chip), also known as Location Analysis (LA), is a high throughput (genome-wide) identification and analysis of DNA fragments that are bound by specific proteins such as histones, transcriptional factors. ChIP-on-chip invovles the following procedures: 1) crosslinking DNA with proteins; 2) sonication of DNA into small pieces; 3) immunoprecipitation of DNA-bound proteins with an antibody; 4) purification of DNA; 5)hybridization of DNA with DNA microarrys.

Protocols
  • A Guideline for ChIP - Chip Data Quality Control and Normalization (Matthias Siebert, Michael Lidschreiber, Holger Hartmann, and Johannes Soding)
    ChIP-on-chip is a powerful technique to measure genome-wide binding sites for proteins of interest. Despite having become very popular during the last 5 or so years, the data analysis is far from being standardized, and many different combinations of methods are being applied. This guideline attempts to give an orientation in the multitude of data transformation and normalization methods employed, by giving clear recommendations for or against using various procedures or by suggesting improvements
    http://www.epigenome-noe.net/researchtools/protoco...
    Added: Thu Feb 25 2010, Hits: 2031, Reviews: 0  Write review  
  • Basic Analysis of NimbleGen ChIP-on-chip Data using Bioconductor/R (Epigenome Network of Excellence)
    This protocol mainly aims to get a rather unbiased look at the quantitative data of NimbleGen tiling array experiments during initial processing steps. Ultimately, summary tracks of the profiles will be generated that permit visual browsing of the data, which serves as important inspiration for downstream analyses.
    http://www.epigenome-noe.net/researchtools/protoco...
    Added: Wed May 27 2009, Hits: 382, Reviews: 0  Write review   Cached
  • ChIP-Chip Protocol (OpenWetWare)
    This protocol is used with Chromatin Immunoprecipitation to detect the in vivo chromatin binding sites of a protein of interest.
    http://openwetware.org/wiki/ChIP/Chip
    Added: Tue Jan 27 2009, Hits: 4150, Reviews: 0  Write review   Cached
  • ChIP-on-chip for Drosophila PDF file (Furlong Lab, EMBL)
    http://furlonglab.embl.de/methods/extras/ChIP-on-c...
    Added: Sat Feb 21 2009, Hits: 1096, Reviews: 0  Write review  
  • Comparison of Sample Preparation Methods for ChIP-chip Assays PDF file (Genome Center, UC Davis)
    Compares three ChIP sample preparation methods that differ in the background noise and reproducibility of binding site identification including LM-PCR, Pooling ChIP samples and whole genome amplification (WGA).
    http://www.genomecenter.ucdavis.edu/expression_ana...
    Added: Tue Jan 27 2009, Hits: 1515, Reviews: 0  Write review  
  • Genome-Scale micro-ChIP-chip Using 10,000 Cells (BioTechniques)
    This miniaturized ChIP protocol using 10,000 cells (without the addition of carrier reagents) can be used to obtain enough sample material to analyze the entire human genome.
    http://www.biotechniques.com/default.asp?page=aop&...
    Added: Tue Jan 27 2009, Hits: 1463, Reviews: 0  Write review   Cached
  • High-Throughput Screening of Chromatin Immunoprecipitates Using CpG-Island Microarrays PDF file (Genome Center, UC Davis)
    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.
    http://www.genomecenter.ucdavis.edu/expression_ana...
    Added: Tue Jan 27 2009, Hits: 765, Reviews: 0  Write review  
  • Protocol for ChIP-on-chip Experiments (ChIP-on-chip.org)
    This multipart protocol describes procedures for 1) Cross-linking of cells and fragmentation and immunoprecipitation of chromatin; 2) Blunting, ligation of linkers to DNA, and amplification by PCR; 3) Labeling of DNA and microarray hybridization; 4) Microarray analysis and identification of in vivo DNA binding sites
    http://www.chiponchip.org/protocol.html
    Added: Tue Jan 27 2009, Hits: 1615, Reviews: 0  Write review   Cached
  • Whole Genome Amplification (WGA) Protocol for ChIP-chip (Epigenome Network of Excellence)
    Based on the low background, reproducibility, and the fact that a single WGA amplified ChIP sample can provide sufficient material for several array hybridizations, we recommend the WGA protocol for ChIP-chip analyses. We have successfully tested our new ChIP amplification protocol on a variety of different factors (E2F family members, KAP1, CtBP2, ZNF217) as well as on histone modifications (H3me3K9, H3me3K27, H3me3K4).Another benefit of the WGA amplification method is the ability to perform a second round of amplification from the initial WGA product if a higher DNA yield is required.
    http://www.epigenome-noe.net/researchtools/protoco...
    Added: Tue Jan 27 2009, Hits: 497, Reviews: 0  Write review   Cached
  • Yeast ChIP-on-Chip PDF file (DeRisi Lab, Dept. of Biochemistry & Biophysics, Univ. of California at San Francisco)
    Protocol for isolation of DNA associated with DNA binding proteins by crosslinking and subsequent immunoprecipitation
    http://www.microarrays.org/pdfs/BeadBeat_IP.pdf
    Added: Tue Sep 24 2002, Hits: 1022, Reviews: 0  Write review