Maskless photolithographic synthesis oligonucleotide array on glass This series of microarrays is designed to represent sense and antisense strands of the nonrepetitive DNA of the human genome with 36mer oligonucleotide probes, positioned every 46nt on average. The probes were selected from the November 14, 2002 human genome sequence assembly (NCBI Build 31/hg13). 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 = genomic tiling, maskless photolithography
Chromosome from which the oligonucleotide sequence was selected
POSITION
Chromosome start position of the oligonucleotide relative to NCBI Build 31, Nov. 14, 2002 (hg13)
STRAND
Sense or antisense strand of the chromosome sequence represented by the oligonucleotide probe
SEQUENCE
DNA sequence of the oligonucleotide
FREQUENCY
Oligomer frequency information calculated to determine the uniqueness of every 36mer subsequence in the genome. This measure was used to select probes that occur fewer than 5 times on average to reduce the potential for cross-hybridization.
