Whole Genome Amplification


GenomePlex® Amplification of ChIP DNA

Intergrated Solutions for ChIP–chip Amplify to ArrayTestimonial
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ChIP-chip is a powerful tool that combines chromatin immunoprecipitation (ChIP) with microarrays to study protein-DNA interactions genome-wide. The ChIP step utilizes an antibody directed against a target protein of interest, such as a transcription factor, polymerase, or modified histone present in nucleosomes. The ChIP step results in the enrichment of DNA fragments bound by the target protein. Normally ChIP DNA samples contain very small amounts of DNA, necessitating the need to amplify the samples before labeling and hybridization to a microarray. For researchers, the GenomePlex Whole-genome Amplification Kits from Sigma-Aldrich® are the preferred method for the efficient, unbiased, amplification of these precious samples. Once amplified, the ChIP DNA is labeled and hybridized to one of Roche NimbleGen's sensitive, high-density (with ≤2.1 million, long-oligonucleotides probes) ChIP-chip microarrays producing the most complete, high resolution maps of protein-DNA interactions across the genome. For more information, please visit the Roche NimbleGen ChIP-chip array webpages.

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Roche NimbleGen is Sigma's preferred partner for ChIP-chip microarrays, providing the most sensitive ChIP-chip microarrays and services available, which are the ChIP-chip platform of choice as supported by the ever-growing list of ≥130 peer-reviewed publications. To facilitate epigenetic research, multiple NimbleGen ChIP-chip microarray designs are available including whole-genome tiling and biologically focused promoter arrays for many organisms. Together with the GenomePlex WGA Kits from Sigma-Aldrich, these tools will produce the most comprehensive maps of target protein DNA binding sites across your genome of interest.


"I have used WGA2 kit to amplify my Chipped DNA. I got brilliant results and amplification was very efficient. Rcommend others to use the same kit in case they want to have reliable and fast results. WGA4 was very good on a small-scale, when I used micro amounts of Chipped DNA from Cell culture. I work with plants and its not easy sometimes to get a proper kit, but WGA kits were perfect!"
Lena M.
Swiss Federal Institute of Technology Zurich (ETH)
Institute of Plant, Animal and Agroecosystem Sciences (IPAS)

Sigma® Roche NimbleGen ChIP-Chip References

Active promoters and insulators are marked by the centrosomal protein 190
Bartkuhn, M. et al. EMBO J. 2009 Apr 8, 28(7), 877-88.
(PubMed abstract)

Genome-Wide Association of Histone H3 Lysine Nine Methylation with CHG DNA Methylation in Arabidopsis thaliana
Bernatavichute, Y. V. et al. PLoS ONE 2008, Sept 8, 3(9).
(PubMed abstract)

Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions
Bushey, A. M. et al. Genes Dev. 2009 Jun, 23(11), 1338–50.
(PubMed abstract)

Evolutionary descent of a human chromosome 6 neocentromere: A jump back to 17 million years ago
Capozzi, O. et al. Genome Res. 2009 May, 19(5), 778–84.
(PubMed abstract)

N-Myc Regulates a Widespread Euchromatic Program in the Human Genome Partially Independent of Its Role as a Classical Transcription Factor
Cotterman, R. et al. Cancer Res. 2008, Dec 1, 68(23), 9654–62.
(PubMed abstract)

Fast genomic µChIP-chip from 1,000 cells
Dahl, J. A. et al. Genome Biology 2009 Feb 10, 10(2):R13.
(PloS Biol abstract)

Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation
Hiratani, I. et al. PLoS Biol 2008, Oct 7, 6(10):e245.
(PubMed abstract)

ING4 Mediates Crosstalk between Histone H3K4 Trimethylation and H3 Acetylation to Attenuate Cellular Transformation
Hung, T. et al. Molecular Cell 2009 Jan 30, 33(2), 248–56.
(PubMed abstract)

Identification of Dlk1, Ptpru and Klhl1 as novel Nurr1 target genes in meso-diencephalic dopamine neurons
Jacobs, F. M. et al. Development 2009 Jul, 136(14), 2363–73.
(PubMed abstract)

Genome-Wide Mapping of Boundary Element-Associated Factor (BEAF) Binding Sites in Drosophila melanogaster Links BEAF to Transcription
Jiang, N. et al. Mol. Cell. Bio. 2009 Jul, 29(13), 3556–68.
(PubMed abstract)

Genome-wide replication profiles indicate an expansive role for Rpd3L in regulating replication initiation timing or efficiency, and reveal genomic loci of Rpd3 function in Saccharomyces cerevisiae
Knott, S. R. et al. Genes Dev. 2009 May 1, 23(9), 1077–90.
(PubMed abstract)

The HBS1L-MYB intergenic interval associated with elevated HbF levels shows characteristics of a distal regulatory region in erythroid cells
Wahlberg, K. et al. Blood 2009 Jun 15. Epub ahead of print.
(PubMed abstract)

Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells
Wen, B. et al. Nat. Genet. 2009 Feb, 41(2), 246–50.
(PubMed abstract)

Comparison of sample preparation methods for ChIP-chip assays
O'Geen, H. et al. BioTechniques 2006 Nov, 41(5), 577–80.
(PubMed abstract)

A novel role for the Aurora B kinase in epigenetic marking of silent chromatin in differentiated postmitotic cells
Sabbattini, P. et al. EMBO J. 2007 Nov 14, 26(22), 4657–69.
(PubMed abstract)

Genome-scale ChIP-chip analysis using 10,000 human cells
Acevedo, L. G. et al. BioTechniques 2007 Dec, 43(6), 791–7.
(No PubMed abstract available)

For more information about Roche NimbleGen Arrays visit: www.nimblegen.com/wga


Whole Genome Amplification Protocol for ChIP-chip (40 Kb PDF)
This protocol is provided courtesy of Dr. Peggy Farnham,
Associate Director of the UC Davis Genome Center
Professor of Pharmacology, UC Davis School of Medicine

The lab of Dr. Peggy Farnham
UC Davis Genome Center Expression Analysis Core Facility

Collaboration with the Buck Institute: ChIP-Chip Analysis using GenomePlex-amplified Genomic DNA. (155 Kb PDF)

NEW! Labeling Protocols for Microarrays
  • Affymetrix WGA ChIP on Chip (361 Kb PDF)
  • NimbleGen™ WGA ChIP on Chip Application Note (569 Kb PDF)

ChIP Workflow


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