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Platform GPL7501 Query DataSets for GPL7501
Status Public on Oct 31, 2008
Title Custom Nimblegen aCGH chip targeted to canFam2 segmental duplications.
Technology type spotted oligonucleotide
Distribution custom-commercial
Organism Canis lupus familiaris
Manufacturer Nimblegen
Manufacture protocol Normal Nimblegen parameters were used with relaxed repeat constraints to enable probe placement in segmental duplication regions.
Support unknown
Coating unknown
 
Description Segmental duplications were computationally identified and then were targeted with 368,360 probes. The remaining available probes were placed in 5kb flanking regions to the segmental duplications (9,278 probes) and in single copy control regions (8,790 probes).
 
Contributor(s) Nicholas TJ, Cheng Z, Ventura M, Mealey K, Eichler EE, Akey JM
Submission date Oct 17, 2008
Last update date Oct 31, 2008
Contact name Thomas J Nicholas
E-mail(s) tjn3@u.washington.edu
Phone 206 897-1846
Fax 206 897-1846
Organization name University of Washington
Department Genome Sciences
Lab Akey Lab
Street address 1705 NE Pacific St. Foege Building
City Seattle
State/province WA
ZIP/Postal code 98195
Country USA
 
Samples (19) GSM334814, GSM334815, GSM334816, GSM334817, GSM334818, GSM334819 
Series (1)
GSE13266 Canine CNVs associated with canFam2 segmental duplications

Data table header descriptions
ID
DESIGN REGION A parameter designating a region for which probes were requested.
REGION TYPE Description of the region for which probes were requested. SEGDUP refers to segmental duplication regions. FLANK refers to regions flanking segmental duplications. CONTROL refers to single copy control regions.
GB_RANGE Probe position in RefSeq accession [start..end]
PROBE POSITION Describes the actual canFam2 genomic location of the probe as "chromosome"."start position of probe".
PROBE LENGTH The length of the probe in basepairs.
PROBE SEQUENCE The sequence of the specified probe.
SPOT_ID

Data table
ID DESIGN REGION REGION TYPE GB_RANGE PROBE POSITION PROBE LENGTH PROBE SEQUENCE SPOT_ID
1 chr1:3000000-3091673 SEGDUP NC_006583.2[3000891..3000940] chr1.3000891 50 AACAATGCAAACAGGAGGGTATACCCAGGTGCAGTAGATTGGTTATCTGG
2 chr1:3000000-3091673 SEGDUP NC_006583.2[3002361..3002413] chr1.3002361 53 AAGTTAACAATGCAAACAGGAGGGTATACCCAGGTGCAGTAGATTGGTTATCT
3 chr1:3000000-3091673 SEGDUP NC_006583.2[3006126..3006175] chr1.3006126 50 ACCTTCTCACTTCCATAGGAATGGGGCTAGTTGACAGCGGGCTTCAAGAC
4 chr1:3000000-3091673 SEGDUP NC_006583.2[3006556..3006605] chr1.3006556 50 CAAGACTAGCGCCTCCAAGCAGAGTCCAGCGTTTTCCGAGTAATTCCTGT
5 chr1:3000000-3091673 SEGDUP NC_006583.2[3007696..3007745] chr1.3007696 50 TCCTGCCTGAGTGTAGACGTAGCTAACACCCTCATGTTAGTTGCTGGGAG
6 chr1:3000000-3091673 SEGDUP NC_006583.2[3007866..3007915] chr1.3007866 50 AGTGGGTAGCCGACTTCTGCCTCCCAGGAATACACAGTTCTGACAGTTGA
7 chr1:3000000-3091673 SEGDUP NC_006583.2[3008426..3008475] chr1.3008426 50 GCATCCTACCTGAGTGTAGACGTAGCTAACACCCTCATATTAGTGGCTGG
8 chr1:3000000-3091673 SEGDUP NC_006583.2[3008736..3008785] chr1.3008736 50 AGAGGTAATTGGAAGCTCCCAGCACACAAGACTAGAGCCTCCAAGCTCAA
9 chr1:3000000-3091673 SEGDUP NC_006583.2[3008851..3008900] chr1.3008851 50 GGTAGTTGAACGCCATGTCCAATAGCATCTCCCTTTTGAGAGTTGAGCTC
10 chr1:3000000-3091673 SEGDUP NC_006583.2[3009156..3009205] chr1.3009156 50 CCGCATCCTACCTGAGTGTAGACGTAGCTGCCAACACCCTCATGTTAGTG
11 chr1:3000000-3091673 SEGDUP NC_006583.2[3009886..3009935] chr1.3009886 50 CCCTCCCGCATACTGACTGTAGACATTCGTCCTGGCATCGTTATGTTAGG
12 chr1:3000000-3091673 SEGDUP NC_006583.2[3010046..3010095] chr1.3010046 50 GGTTCTAGCTCCCCTGTGTAAGTGTCTGGCAGACATCTGCCTGCAAAGCG
13 chr1:3000000-3091673 SEGDUP NC_006583.2[3010621..3010670] chr1.3010621 50 CCTCCCGCATACTGACTGTAGACATTCGTCCTGGCATCGTTATGTTAGGT
14 chr1:3000000-3091673 SEGDUP NC_006583.2[3010731..3010782] chr1.3010731 52 GGTCAATATAGCGATTGCTAACATCCTTGTTCAATCAGAGAGTAGCTCGGTT
15 chr1:3000000-3091673 SEGDUP NC_006583.2[3011036..3011095] chr1.3011036 60 TCCATACGTGAGAAAGTAGCTGAACGACTTGTCCAAAATCAACATATTTCTTAGAGTTGA
16 chr1:3000000-3091673 SEGDUP NC_006583.2[3011776..3011825] chr1.3011776 50 TATGGCCTGTATCTCCCACATCCTGCCTGAAGGTACACTTCGCTCTTAAC
17 chr1:3000000-3091673 SEGDUP NC_006583.2[3011931..3011985] chr1.3011931 55 CCTGTCTTAGACTGGTGCTTACATACTAAATTCCATACGTCAGAAGGTATCTGAA
18 chr1:3000000-3091673 SEGDUP NC_006583.2[3012046..3012095] chr1.3012046 50 GAGTTTCAAACATCTTGACCAGAGACGTTTGTCAGATACTGGAGAGACGC
19 chr1:3000000-3091673 SEGDUP NC_006583.2[3012221..3012270] chr1.3012221 50 TCTAGGCATGTTTCGTTGTGAGAACTGAGGTCAGGGCATGACCCTCCTGC
20 chr1:3000000-3091673 SEGDUP NC_006583.2[3012351..3012409] chr1.3012351 59 GACAGGCTTGTACTCTCCTGTATCTCATTTCAATACAGCGATTATGAACACGTATAATG

Total number of rows: 386428

Table truncated, full table size 51302 Kbytes.




Download family Format
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Supplementary file Size Download File type/resource
GPL7501_071025_CanFam2_U_Wash_cgh.ndf.gz 24.8 Mb (ftp)(http) NDF
GPL7501_071025_CanFam2_U_Wash_cgh.pos.gz 5.2 Mb (ftp)(http) POS

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