title: Human 36mer ENCODE region oligonucleotide tiling array (Yale design #1)
status: Public on May 24 2005
contact.city: New Haven
contact.first: Olof
contact.last: Emanuelsson
contact.email: olofe@sbc.su.se
contact.state: CT
contact.address: 260 Whitney Avenue
contact.country: USA
contact.institute: Yale University
contact.phone: +1-203-432-6105
organism: Homo sapiens
description: Maskless photolithographic synthesis oligonucleotide array on glass.
  
  This series of microarrays is designed to represent sense (FWD) and antisense (REV) strands of the nonrepetitive DNA of the human ENCODE pilot regions with 36mer oligonucleotide probes, positioned every 36nt on average (end to end tiling). The probes were selected from the July 2003 human genome sequence assembly (NCBI Build 34/hg16).
  
  This design covers ENm001-ENm011 and parts of ENm012. In addition to the ENCODE regions, the nonrepetitive part of three RefSeq genes, ATP6AP1 (NM_001183), PSMD4 (NM_002810), and ARF5 (NM_001662) were tiled at one nucleotide resolution.
  
  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 390,000 oligonucleotide features in a 14 × 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.
  
  Keywords = ENCODE, tiling array, maskless photolithography
manufacture_protocol: Maskless photolithographic synthesis oligonucleotide array on glass