DNA microarrays manufactured by YiPeng Wang and Michael McClelland



Human Promoter Array (PCR products)


Human promoter sequences (1000bp upstream and 500bp downstream from transcription initiation site) were retrieved batch-wise from GoldenPath. Promoter fragments with an average length of 900 base pairs were amplified, purified and spotted onto UltraGAPS coated slides (Corning Incorporated, Corning, NY) in the presence of 50% DMSO. Promoters were printed on two slides, set A and set B. Each slide contains 6400 spots spotted at three separate arrays. In total, these two promoter microarrays contains 12186 promoter sequences (including 192 oligos), 544 non-promoter controls, 32 salmonella controls, 32 CyDye 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, J., et al, 2004, Wang, Y., et al, 2005, Wang, Y., et al, 2005, and Arora et al., 2008).


Details about the oligonucleotide probes can be downloaded here.


Human Promoter Oligo Array (NimbleGen Platform) in collaboration with Fred Long.


NimbleGen oligonucleotide arrays were custom designed for whole genome methylation analysis in a high-resolution manner. 1) Human genome sequences were downloaded from UCSC Golden Path Database based on NCBI Build 35. HpaII fragments (sequences between two CCGG sites) shorter than 500bp and longer than 50bp were extracted. Fragments overlapping with the putative promoter region (between transcription start site and its upstream 5000bp sequences) were kept for oligonucleotide probe design; 2) Sequences were repeat-masked; 3) Probes were designed from the sense strand of the non-repeat-masked portions of the promoter regions, with these probe restrictions: a) Length: 46 - 50 bases; b) Tm: 69 - 79oC; c) Manufacture by NimbleGen within 148-rounds of A, C, G, T; d) Probe must not contain simple repeats (AAAAAAA, TTTTTTTT, CCCCCCCC, GGGGGGGG, GTGTGTGT, or CACACACA); e) Probe must not have tendency to form strong structures; 4) Probe specificity was screened by aligning them to the human genome using Blat. Probes that had imperfect matches in the genome of 30 bases or more were thrown out, as were probes that had more than 2 exact matches; 5) Oligonucleotides in promoters of genes with known functions were given priority; 6) probe spacing of 23 bases were used to filter probes and in the cases of less than 3 probed within two CCGG site, probe spacing of 10 bases were used. The final 355,264 selected oligonucleotide probes represent 18212 HpaII fragments (corresponding to 12,617 refSeq genes, average 28 probes per promoter). 57.34% (10,443/18,212) sequences overlap with CpG islands, 42.66% (7,769/18,212) do not.


Details about the oligonucleotide probes can be downloaded here.