title: Sidney Kimmel Cancer Center Human Promotor 19K Array, v13, set-A
status: Public on Feb 05 2008
contact.city: San Diego
contact.first: Yipeng
contact.last: Wang
contact.email: ywang@sdibr.org
contact.state: CA
contact.country: USA
contact.institute: Vaccine Research Institute of San Diego
contact.phone: 8585813960
organism: Homo sapiens
manufacture_protocol: Human promoter sequences (1000bp upstream and 500bp downstream from transcription initiation site) were utilized for fabrication of the arrays.  Approximately 5000 sequences were retrieved batch-wise from GoldenPath. Primers for amplification of these sequences were generated batchwise using Primer 3 (Rozen and Skaletsky 2000) designed to generate an average amplicon of 1200 nts. An additional ~ 13,000 sequences were prepared using the primer set developed by the Whitehead Institute Center for Microarray Technology (http://www.wi.mit.edu/CMT/Downloads.html) designed to generate and average amplicon of ~840 nts. The promoter sequences were amplified purified and spotted onto UltraGAPS coated slides (Corning Incorporated, Corning, NY) in the presence of 50% DMSO. The products of all amplification were visualized by agarose gel electrophoresis. Over 70% of all amplifications yielded single products of the expected size.  Failed amplifications were recorded and ignored in the subsequent robot-assisted selection for spotting using Biomek FX (Beckman Coulter, Inc). Promoter arrays were printed on two slides, set A and set B. Each array contains triplicate of 6400 spots. In total, promoter microarray contains 12186 promoter sequences (including 192 oligos), 544 non-promoter controls, 32 salmonella controls, 32 Cy Dye controls and 6 blank spots. Many of the promoters on the array are from genes of particular relevance to cancer and the array includes promoters from most of the genes that are known to be regulated by methylation in cancer. Human promoter array have been used for high-throughput DNA methylation assay and ChIP-on Chip analysis (Hayakawa, Mittal et al. 2004; Wang, Hayakawa et al. 2005).