title: CSHL-Human-MOMA2, 368K CpG tiling array
status: Public on Apr 28 2009
contact.city: Cold Spring Harbor
contact.first: Robert
contact.last: Lucito
contact.email: lucito@cshl.edu
contact.state: NY
contact.address: 1 Bungtown Road
contact.department: Genome Center
contact.country: USA
contact.institute: Cold Spring Harbor Laboratory
organism: Homo sapiens
manufacture_protocol: Our approach to map genome-wide methylation involves tiling all the predicted CpG islands. All annotated CpG islands were obtained from the UCSC genome browser. These islands were predicted using the published Gardiner-Garden and Frommer (1) definition and involves the following criteria: length >= 200bp, %GC >= 50%, observed/expected CpG >= 0.6. There are ~26219 CpG islands in the range of 200bp to 2000bp in the genome. These islands are well covered by Msp I restriction fragmentation. Arrays were manufactured by Nimblegen Systems Inc using the 390K format to the following specifications. The CpG island annotation from human genome build 33 (hg17) was used to design a 50 mer tiling array. The 50 mers were shifted on either side of the island sequence coordinates to evenly distribute the island. The 390K format has 367,658 available features which would not fit all islands with a 50 mer tiling. Therefore we made a cutoff on the islands to be represented based on size, with only CpG islands of size 200b-2000b being assayed. The array represents classical CpG islands and does not include imprint control regions or other non-island promoters known to be methylated. Background hybridization signal could be high with probes of high GC content since by definition these probes will be. Therefore, control probes which are not in a MspI representation were designed to represent background signal, and these probes were used to calculate signal to noise