The Farnham Laboratory

Microarray binding analysis

The Farnham lab has developed a technique that allows the direct identification of novel genomic targets of mammalian DNA binding factors by coupling chromatin immunoprecipitation with CpG-island microarray analysis:

Weinmann, A.S., Yan, P.S., Oberley, M.J., Huang, T.H., and Farnham, P.J. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarry analysis. Genes Dev. 16: 235-244, 2002. [Abstract] [pdf].

Wells J., Yan P.S., Cechvala M., Huang T., Farnham P.J. Identification of novel pRb binding sites using CpG microarrays suggests that E2F recruits pRb to specific genomic sites during S phase. Oncogene. 22: 1445-60, 2003.[Abstract] [pdf].

Oberley M.J., Inman D.R., Farnham P.J. E2F6 negatively regulates BRCA1 in human cancer cells without methylation of histone H3 on Lysine 9. J Biol Chem. 278: 42466-76, 2003).[pdf]

Oberley MJ, Tsao J, Yau P, Farnham PJ. High-Throughput Analysis of Chromatin Immunoprecipitates. Methods in Enzymology. 376: 316-335, 2003.[pdf]

See protocols section for our latest ChIP-chip protocol.