Oligo nucleotides 36mer in length are designed to represent sense and antisense strands of the nonrepetitive DNA of the japonica and indica rice chromosome 10. The probes were selected from the April 12, 2004 japonica genome sequence (TIGR rice annotation 2.0) and the August 1, 2003 indica sequence from BGI. Microarrays containing these oligos are synthesized on glass with Expedite DNA synthesizers (Applied Biosystems, Foster City, CA) in conjunction with Maskless Array Synthesis units (NimbleGen Systems, Madison, WI).
Tiling microarray analysis of japonica and indica rice chromosome 10
Data table header descriptions
ID
X
X coordinate of the oligo feature
Y
Y coordinate of the oligo feature
CHR
Chromosome from which the oligonucleotide sequence was selected
POSITION
Chromosome start position of the rice pseudomolecules release 2 by TIGR
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
