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Platform GPL13483 Query DataSets for GPL13483
Status Public on Jul 27, 2011
Title Arabidopsis thaliana AtSNPtile 1
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Arabidopsis thaliana
Manufacturer Affymetrix
Manufacture protocol see web site
 
Description This array contains both SNP probes and tiling probes. SNP probes interrogate ~250K SNPs obtained from resequencing of 20 diverse Arabidopsis thaliana strains (Clark et al. 2007). Each SNP is interrogated by the middle base of four 25mer probes, representing 2 alleles on 2 strands. Tiling probes interrogate ~1.5M unique sequences tiled along the Arabidopsis thaliana genome with ~35 bp resolution. The reference genome for the array design is Columbia-0. The array is based on The Arabidopsis Information Resource (TAIR) genome release TAIR9.
 
Submission date May 03, 2011
Last update date Jul 27, 2011
Contact name Fei He
E-mail(s) [email protected]
Organization name Institute for Evolution and Biodiversity
Department Münster University
Lab de Meaux
Street address Hüfferstr. 1
City Münster
ZIP/Postal code 48149
Country Germany
 
Samples (24) GSM719401, GSM719402, GSM719403, GSM719404, GSM719405, GSM719406 
Series (1)
GSE29037 Allele-specific expression between Arabidopsis genus

Data table header descriptions
ID
SNP_ID
SEQUENCE
CHROMOSOME
BP
ALLELE
STRAND
PROBE_TYPE
RANGE_GB
RANGE_STRAND
RANGE_START
RANGE_END

Data table
ID SNP_ID SEQUENCE CHROMOSOME BP ALLELE STRAND PROBE_TYPE RANGE_GB RANGE_STRAND RANGE_START RANGE_END
X783_Y216_1_657_C_T 1_657_C_T CTCGACGATGCTCTATTTCTATCCT 1 657 C antisense SNP NC_003070.5 - 645 669
X15_Y426_1_657_C_T 1_657_C_T AGGATAGAAATAGAGCATCGTCGAG 1 657 C sense SNP NC_003070.5 + 645 669
X783_Y215_1_657_C_T 1_657_C_T CTCGACGATGCTTTATTTCTATCCT 1 657 T antisense SNP NC_003070.5 - 645 669
X15_Y425_1_657_C_T 1_657_C_T AGGATAGAAATAAAGCATCGTCGAG 1 657 T sense SNP NC_003070.5 + 645 669
X1526_Y630_1_3102_A_G 1_3102_A_G GCGTGTTCACACACATAATCTAGAA 1 3102 A antisense SNP NC_003070.5 - 3090 3114
X1207_Y316_1_3102_A_G 1_3102_A_G TTCTAGATTATGTGTGTGAACACGC 1 3102 A sense SNP NC_003070.5 + 3090 3114
X1526_Y629_1_3102_A_G 1_3102_A_G GCGTGTTCACACGCATAATCTAGAA 1 3102 G antisense SNP NC_003070.5 - 3090 3114
X1207_Y315_1_3102_A_G 1_3102_A_G TTCTAGATTATGCGTGTGAACACGC 1 3102 G sense SNP NC_003070.5 + 3090 3114
X832_Y386_1_4648_C_A 1_4648_C_A GAGTAGGCAGATCAAAAAAGAGCTT 1 4648 C antisense SNP NC_003070.5 - 4636 4660
X1460_Y178_1_4648_C_A 1_4648_C_A AAGCTCTTTTTTGATCTGCCTACTC 1 4648 C sense SNP NC_003070.5 + 4636 4660
X832_Y385_1_4648_C_A 1_4648_C_A GAGTAGGCAGATAAAAAAAGAGCTT 1 4648 A antisense SNP NC_003070.5 - 4636 4660
X1460_Y177_1_4648_C_A 1_4648_C_A AAGCTCTTTTTTTATCTGCCTACTC 1 4648 A sense SNP NC_003070.5 + 4636 4660
X1540_Y248_1_4880_C_T 1_4880_C_T GGCGGTCAGTGGCTGAGTGACTATA 1 4880 C antisense SNP NC_003070.5 - 4868 4892
X995_Y100_1_4880_C_T 1_4880_C_T TATAGTCACTCAGCCACTGACCGCC 1 4880 C sense SNP NC_003070.5 + 4868 4892
X1540_Y247_1_4880_C_T 1_4880_C_T GGCGGTCAGTGGTTGAGTGACTATA 1 4880 T antisense SNP NC_003070.5 - 4868 4892
X995_Y99_1_4880_C_T 1_4880_C_T TATAGTCACTCAACCACTGACCGCC 1 4880 T sense SNP NC_003070.5 + 4868 4892
X1285_Y574_1_5975_T_G 1_5975_T_G ACCAAAGTTGCATTTGCAAGGAAAT 1 5975 T antisense SNP NC_003070.5 - 5963 5987
X1580_Y442_1_5975_T_G 1_5975_T_G ATTTCCTTGCAAATGCAACTTTGGT 1 5975 T sense SNP NC_003070.5 + 5963 5987
X1285_Y573_1_5975_T_G 1_5975_T_G ACCAAAGTTGCAGTTGCAAGGAAAT 1 5975 G antisense SNP NC_003070.5 - 5963 5987
X1580_Y441_1_5975_T_G 1_5975_T_G ATTTCCTTGCAACTGCAACTTTGGT 1 5975 G sense SNP NC_003070.5 + 5963 5987

Total number of rows: 994336

Table truncated, full table size 117238 Kbytes.




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