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).
Description
This experiment was designed to identify transcribed regions of japonica subspecies of the rice genome. A series of high-density oligonucleotide tiling arrays that represent sense and antisense strands of the entire nonrepetitive sequence of all the 12 chromosomes were designed to measure genome-wide transcription. A total of 12253842 36mer oligonucleotide probes positioned every 46 nt on average were used for this purpose. The probes were synthesized via maskless photolithography at a feature density of approximately 389,000 probes per slide. The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA population (seedling root, seedling shoot, panicle, and suspension cultured cells).
Tiling microarray of Oryza sativa japonica at 46nt resolution
Data table header descriptions
ID
X
X coordinate of the array feature
Y
Y coordinate of the array feature
CHROMOSOME
Chromosome from which the oligonucleotide sequence was selected
POSITION
Chromosome start position of the oligonucleotide from version 2 of TIGR rice pseudomolecules, similar but not equivalent to NC_008400.1
STRAND
Sense or antisense strand of the chromosome sequence represented by the oligonucleotide probe
SEQUENCE
DNA sequence of the oligonucleotide
FREQUENCY
Oligomer frequency 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.
