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Platform GPL4816 Query DataSets for GPL4816
Status Public on Feb 21, 2007
Title Tiling microarray for Oryza sativa japonica genome (version 2 pseudomolecules from TIGR) Chromosome 12
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Oryza sativa
Manufacturer NimbleGen Systems, Madison, WI
Manufacture protocol 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 populations (seedling root, seedling shoot, panicle, and suspension cultured cells).
 
Web link http://www.yale.edu/denglab/
Contributor(s) Li L, Wang X, Sasidharan R, Stolc V, Deng W, He H, Korbel J, Chen X, Tongprasit W, Ronald P, Chen R, Gerstein M, Deng X
Submission date Feb 07, 2007
Last update date Feb 21, 2007
Contact name Rajkumar Sasidharan
E-mail(s) rajkumar.sasidharan@yale.edu
Organization name Yale University
Department MB & B
Lab Gerstein
Street address 266 Whitney Avenue
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Samples (1) GSM161100
Series (1)
GSE6996 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_008405.1
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.

Data table
ID X Y CHROMOSOME POSITION STRAND SEQUENCE FREQUENCY
152614 116 738 12 8770844 + TATTATATTTTAGCCGTGACAAAAGGAAGATAAAAT 4.150000
152615 67 57 12 8770887 + GATTTCTACTCTTAAAATTGTTAAATTTCTCAATTT 3.050000
152616 767 347 12 8770985 + ATGTGTAATACTATTAAGAGTATATGTTAGAACTTT 4.350000
152617 747 799 12 8771031 + TGCTAGTTGGCGCGCATGGAAATGTTATGTGCATAG 1.200000
152618 69 591 12 8771077 + CTGTCGTATTTCTTGTTTTACCCAAATTATATCACA 1.050000
152619 361 187 12 8771123 + GTTGTTTGGTTCTTTGCCTCACAAACTTAACCATAC 1.000000
152620 593 101 12 8771169 + GTGTTGCTGAAAATTTTATGCCTTATTTTGTTTGTA 1.150000
152621 250 224 12 8771215 + TGACTGCCTATTTTTTGGTTTGGTTGATTTTAGTTA 1.900000
152622 161 357 12 8771261 + AAATACTCTTTAGTAGGAAACTAAACACTAGCTAGC 1.050000
152623 237 101 12 8771305 + CAACTCTTACTTAAAAAAAAATGGTACTACCTCCGT 3.650000
152624 723 227 12 8771351 + AAGAATTTCTAACATTACCAACATTCATATATATAT 3.650000
152625 230 154 12 8771413 + CTAAATTCATTAATATATATGTAAATGTGAGCAATA 4.450000
152626 114 814 12 8771470 + AACGGAGGGAGTAACAATCTAAACATCTGCAATAGT 4.700000
152627 330 386 12 8771516 + ATTGCCGAAAATTGGCAAGGCTACAAAAAGCATAAC 1.200000
152628 184 516 12 8771562 + CTAAGCAACAACTACATTTTAATCATTCAACATGCC 1.100000
152629 415 493 12 8771608 + CGGGCACGTAACACAAACACGAGAGACAACGTCTCT 1.100000
152630 457 979 12 8771654 + CTGTTATGTGGGTTATCACTTACACGGATAAAAAGC 1.200000
152631 652 816 12 8771700 + TGGATCATCACACACGTTGATTCCAGCCGCGCGTCC 1.000000
152632 650 648 12 8771746 + TTTTCGGGCTAAAAAAACCCAAAAAAATATATCATA 3.200000
152633 343 1023 12 8771792 + AATCCATACACGGTGCCACACAATTTTCACGTTAAA 1.000000

Total number of rows: 287600

Table truncated, full table size 20985 Kbytes.




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