title: Duke/RG_MycMaxMad_v1
status: Public on May 17 2013
contact.city: Worcester
contact.first: Raluca
contact.last: Gordan
contact.email: raluca.gordan@umassmed.edu
contact.state: MA
contact.address: 368 Plantation St, AS5-1059
contact.department: Genomics and Computational Biology
contact.country: USA
contact.institute: University of Massachusetts Chan Medical School
organism: Homo sapiens
description: 180K array. 36-bp probes.
  In situ oligo synthesized array with proprietary synthetic sequences that target Myc/Max/Mad putative binding sites in a genomic context.
  There are three categories of 36-bp sequences: 1) bound probes, 2) unbound probes (or negative controls), and 3) test probes. Bound probes correspond to genomic regions bound in vivo by c-Myc, Max, or Mad2 (ChIP-seq P < 10^(-10) in HeLaS3 or K562 celld (ENCODE)) that contain at least two consecutive 8-mers with universal PBM E-score > 0.4 (Munteanu and Gordan, LNCS 2013). All putative binding sites occurr at the same position within the probes on the array. “Unbound” probes correspond to genomic regions with ChIP-seq P < 10^(-10) and a maximum 8-mer E-score < 0.2. We also designed test probes that contain, within constant flanking regions, all nnCACGTGnn 10-mers and 18 nnnCACGTGnnn 12-mers (where n = A, C, G, or T). Each DNA sequence represented on the array is present in 6 replicate spots.
manufacture_protocol: See manufacturer's website (www.agilent.com).