Display options
Cite
Deatherage DE, Potter D, Yan PS, et al. Methylation analysis by microarray. Methods Mol Biol. 2009;556:117-39doi: 10.1007/978-1-60327-192-9_9.
Deatherage, D. E., Potter, D., Yan, P. S., Huang, T. H., & Lin, S. (2009). Methylation analysis by microarray. Methods in molecular biology (Clifton, N.J.), 556117-39. https://doi.org/10.1007/978-1-60327-192-9_9
Deatherage, Daniel E, et al. "Methylation analysis by microarray." Methods in molecular biology (Clifton, N.J.) vol. 556 (2009): 117-39. doi: https://doi.org/10.1007/978-1-60327-192-9_9
Deatherage DE, Potter D, Yan PS, Huang TH, Lin S. Methylation analysis by microarray. Methods Mol Biol. 2009;556:117-39. doi: 10.1007/978-1-60327-192-9_9. PMID: 19488875; PMCID: PMC2838393.
Copy Download .nbib Format: NLM
Share it on

Methods Mol Biol. 2009;556:117-39. doi: 10.1007/978-1-60327-192-9_9.

Methylation analysis by microarray.

Methods in molecular biology (Clifton, N.J.)

Daniel E Deatherage, Dustin Potter, Pearlly S Yan, Tim H-M Huang, Shili Lin

Affiliations

  1. Human Cancer Genetics Program, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.

PMID: 19488875 PMCID: PMC2838393 DOI: 10.1007/978-1-60327-192-9_9

Abstract

Differential methylation hybridization (DMH) is a high-throughput DNA methylation screening tool that utilizes methylation-sensitive restriction enzymes to profile methylated fragments by hybridizing them to a CpG island microarray. This array contains probes spanning all the 27,800 islands annotated in the UCSC Genome Browser. Herein we describe a DMH protocol with clearly identified quality control points. In this manner, samples that are unlikely to provide good read-outs for differential methylation profiles between the test and the control samples will be identified and repeated with appropriate modifications. The step-by-step laboratory DMH protocol is described. In addition, we provide descriptions regarding DMH data analysis, including image quantification, background correction, and statistical procedures for both exploratory analysis and more formal inferences. Issues regarding quality control are addressed as well.

References

  1. Genome Biol. 2002 Jun 28;3(7):RESEARCH0037 - PubMed
  2. Proc Natl Acad Sci U S A. 2002 Mar 19;99(6):3740-5 - PubMed
  3. Nat Genet. 2001 Dec;29(4):412-7 - PubMed
  4. Cell. 2007 Feb 23;128(4):683-92 - PubMed
  5. Bioinformatics. 2000 Aug;16(8):707-26 - PubMed
  6. J Comput Biol. 2001;8(6):625-37 - PubMed
  7. Biometrics. 2007 Sep;63(3):787-96 - PubMed
  8. Anal Chem. 2003 Sep 1;75(17):4672-5 - PubMed
  9. Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5116-21 - PubMed
  10. BMC Bioinformatics. 2005 Jul 12;6:173 - PubMed
  11. Methods Mol Biol. 2003;224:111-36 - PubMed
  12. Methods Mol Biol. 2009;507:89-106 - PubMed
  13. Bioinformatics. 2001 Jun;17(6):520-5 - PubMed
  14. Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14863-8 - PubMed
  15. Curr Opin Genet Dev. 2005 Oct;15(5):490-5 - PubMed
  16. Bioinformatics. 2003 Jan 22;19(2):185-93 - PubMed
  17. BMC Bioinformatics. 2007 Mar 30;8:111 - PubMed
  18. Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12457-62 - PubMed

Substances

MeSH terms

Publication Types

Grant support