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Platform GPL1937

Query DataSets for GPL1937

Status

Public on Apr 09, 2005

Title

Tiling microarray analysis of rice indica chromosome 10 (forward strand)

Technology type

in situ oligonucleotide

Distribution

non-commercial

Organism

Description

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).
Keywords = transcription
Keywords = gene expression
Keywords = rice

Contributor(s)

Li L, Wang X, Xia M, Stolc V, Su N, Peng Z, Li S, Tongprasit W, Wang J, Wang X, Deng X

Submission date

Mar 31, 2005

Last update date

Jun 16, 2005

Contact name

Xing-Wang Deng

E-mail(s)

xingwang.deng@yale.edu

Phone

203-432-8908

Organization name

Yale University

Department

MCD Biology

Street address

165 Prospect

City

New Haven

State/province

CT

ZIP/Postal code

06520

Country

USA

Samples (1)

Series (1)

Tiling microarray analysis of japonica and indica rice chromosome 10

Data table header descriptions
ID
X	X coordinate of the array feature
Y	Y coordinate of the array 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

Data table
ID	X	Y	CHR	POSITION	STRAND	SEQUENCE	FREQUENCY
1	366	420	10	1	+	CCACTCACATCATATTAAGACAAATGGAGTATGAAT	2.700000
2	614	216	10	47	+	AAATTCTATTTTATATCAATGACAAGAAGCACCCGT	1.350000
3	359	931	10	93	+	TGAATCAGATTTTCATACGTGGGCTAAAATAAGTTT	2.550000
4	438	992	10	139	+	TCTAACTAATTTAAGTAGTTTTTTCATTTATATTAT	2.300000
5	344	412	10	277	+	ATTTTCCTGATATTGAATTATCATTCCCGGCAAAGT	3.800000
6	436	432	10	323	+	TTCATGTTGTTATTTATACGTTTATATTTCCTTCAT	3.700000
7	51	961	10	369	+	CAACTAAGCTTTTAGGGGTACATAGGGGATTTTGTC	4.400000
8	418	338	10	415	+	CCGGAGCCACCACCACAATGAATCTTGGAGAGTGTG	2.200000
9	114	196	10	461	+	ACACTAGCGGACGCGAAGATCTCATAGAGGTGGAGA	1.650000
10	693	501	10	507	+	GGCTGCAGAGGTATATATCCCCTAGGAGGTTGAGCT	2.750000
11	220	22	10	553	+	ACAGAGGGTAAGTAATGAGAGAGAGTCGGGCACGGG	1.050000
12	187	695	10	599	+	GGATGACGACCTACAGGACCACTATTTATTAATCTT	1.000000
13	574	1020	10	645	+	AGATTGTCATGTAGGTGCACATAAGTGAAAACTCTC	1.100000
14	476	514	10	691	+	TATTAGGGTGGATAAAGTGGATATTATAATAGTTGA	1.100000
15	372	152	10	737	+	CTATCCCGAATTTATAGTTGAGGGGTAAATTTTAGA	2.200000
16	241	831	10	783	+	AGTTGAGAAGTGAATAATTTTAAGTATATGTACTTT	2.400000
17	539	779	10	829	+	CCACCCAAGGAGATTGAATTGTCGCCATCAGACATT	1.750000
18	755	249	10	875	+	AGTTCTGGTTCTGTATGATCGGTGATGAGTTGATGG	1.650000
19	606	22	10	921	+	GATCCGGATTCCAATTTTACATGCTTCTCTAAGGAA	2.100000
20	481	347	10	967	+	TTGGCATCTTCTCTAAGGAGATTATTCCTTGCCACT	2.000000

Total number of rows: 336307

Table truncated, full table size 24302 Kbytes.

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Supplementary data files not provided

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