title: Maskless Photolithographic 50mer ENCODE Array (FWD)
status: Public on May 27 2005
contact.city: New Haven
contact.first: Joel
contact.last: Rozowsky
contact.email: rozowsky@csb.yale.edu
contact.state: CT
contact.address: 266 Whitney Ave, Bass 437
contact.department: Molecular Biophysics & Biochemistry
contact.country: USA
contact.institute: Yale University
contact.phone: 203-432-5405
organism: Homo sapiens
description: Maskless photolithographic synthesis oligonucleotide array on glass. This microarray is designed to the forward strand nonrepetitive DNA of the human ENCODE regions with 50mer oligonucleotide probes tiled approximtely end-to-end (oligonucleotides are allowed to shift by several nucleotides to avoid oligomer sequences forming secondary structure). The probes were selected from NCBIv34 (hg16) build of the human genome. Microarrays were constructed with Expedite DNA synthesizers (Applied Biosystems, Foster City, CA) in conjunction with Maskless Array Synthesis (MAS) units (NimbleGen Systems, Madison, WI). Arrays containing approximately 190,000 oligonucleotide features in a 14 mm x 17.4 mm square area were fabricated with photolabile phosophoramidites (NPPOC-dAdenosine (N6-tac) -Cyanoethylphosphoramidite, NPPOC-dCytidine (N4-Isobutyryl) -Cyanoethylphosphoramidite NPPOC-dGuanosine (N2-ipac) -Cyanoethylphosphoramidite, NPPOC-dThymidine-Cyanoethylphosphoramidite) obtained from Proligo (Boulder, CO). Following MAS synthesis, base-protecting groups were removed in a solution of ethylenediamine:ethanol (1:1 v/v) (Aldrich, St. Louis, MO) for 2 hours. The arrays were rinsed with water, dried and stored desiccated until use.
  Keyword: genomic tiling, maskless photolithography