Maskless photolithographic synthesis oligonucleotide array on glass
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 ENm008, ENm013-014, ENr111-213, the backup regions for the manual picks, and parts of ENm012 and ENr221. 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.
Chromosome from which the oligonucleotide was obtained
GENOMIC_POSITION
Chromosomal start position of the oligonucleotide
STRAND
Sense (FWD) or antisense (REV) strand of the oligonucleotide
X-COORD
X coordinate of the array feature
Y-COORD
Y coordinate of the array feature
SEQUENCE
DNA sequence of the oligonucleotide
ENCODE_REGION
Which ENCODE pilot region is the oligonucleotide from (ENm001-014, ENr111-334). Alternatively, which of the three Refseq genes (ATP6AP1, PSMD4, ARF5) tiled at one basepair resolution is the oligonucleotide from.
