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Platform GPL6553 Query DataSets for GPL6553
Status Public on Sep 15, 2008
Title Nimblegen 385K pig array CGH
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Sus scrofa
Manufacturer Nimblegen Systems Inc.
Manufacture protocol Maskless array synthesis was used to construct isothermal arrays. Probes were selected with a minimum probe spacing of 285 bp and the resulting array had a median probe spacing of 409 bp. Probes were synthesized using an isothermal format (Tm = 76°C) and varied in length from 50 to 75 bp.
 
Description The probes on the array covered part of the chromosomes 4, 7, 14 and 17 for the Sus Scrofa preliminary assembly version 3, August 2007. The sequence data were produced by the Sus Scrofa Sequencing Group at the Sanger Institute.
Detailed information about probe design is available in the Nimblegen technical note (see Web Link).
 
Web link http://www.nimblegen.com/products/lit/probe_design_2007_11_13.pdf
Contributor(s) Fadista J, Holm L, Thomsen B, Bendixen C
Submission date Mar 06, 2008
Last update date Sep 15, 2008
Contact name Jakob Hedegaard
E-mail(s) Jakob.Hedegaard@ki.au.dk
Phone (+45)89991363
Organization name Aarhus University, Faculty of Agricultural Sciences
Department Department of Genetics and Biotechnology
Lab Molecular Genetics and System Biology
Street address PO-box 50
City Tjele
ZIP/Postal code DK-8830
Country Denmark
 
Samples (24) GSM271285, GSM271286, GSM271289, GSM271294, GSM271300, GSM271302 
Series (1)
GSE10753 A Snapshot of Copy Number Variation in the pig genome

Data table header descriptions
ID
CONTAINER The container for each probe
DESIGN_NOTE A comment field suitable for placing information necessary to data analysis
SELECTION_CRITERIA How a probe was selected
SEQ_ID The NimbleGen sequence identifier
SEQUENCE Contains the DNA sequence synthesized on the microarray
MISMATCH The mismatch index of the PROBE_SEQUENCE. This value is 0 for the perfect match probe, 1 for the first mismatch and so on
MATCH_INDEX An integer that ties sets of probes
FEATURE_ID An integer that uniquely identifies an aggregate feature
ROW_NUM An integer that represents the Y coordinate of the feature within its CONTAINER
COL_NUM An integer that represents the X coordinate of the feature within its CONTAINER
PROBE_CLASS For internal use, to record a value of experimental fiducial control
PROBE_ID The NimbleGen probe identifier
POSITION An integer that indicates the position of the PROBE_SEQUENCE in the target sequence or region of interest, starting from the left or 5´end
DESIGN_ID The NimbleGen-assigned identifier for the design
X An integer that indicates the X coordinate of the feature on the image
Y An integer that indicates the Y coordinate of the feature on the image

Data table
ID CONTAINER DESIGN_NOTE SELECTION_CRITERIA SEQ_ID SEQUENCE MISMATCH MATCH_INDEX FEATURE_ID ROW_NUM COL_NUM PROBE_CLASS PROBE_ID POSITION DESIGN_ID X Y
6394_0446_0002 BLOCK1 interval rank target_tm:76.00;probe_tm:75.80;freq: 2.62;count:01;rules:0000;score:0926 chr4:1-52983990 TGGAAACCTAGGCACTCTGACAACCATTCCCAGGAAACTACAAAGAGAAAA 0 64187516 64187516 2 446 experimental CHR04FS015922764 15922764 6394 446 2
6394_0448_0002 BLOCK1 interval rank target_tm:76.00;probe_tm:75.50;freq: 2.13;count:01;rules:0000;score:0936 chr7:1-76062954 TTATTGCCTTGGTTCATATTCTTCCAACTTCTTCTCAAGCACTTTAAGCAGAACAGCAATG 0 64333887 64333887 2 448 experimental CHR07FS054140626 54140626 6394 448 2
6394_0450_0002 BLOCK1 interval rank target_tm:76.00;probe_tm:75.70;freq: 4.50;count:01;rules:0000;score:0886 chr17:1-25535214 ATGACATCACTTGAGAACCTGGATCCAGCCATTCCTGAAGCACATTAGTTTT 0 64532740 64532740 2 450 experimental CHR17FS017898678 17898678 6394 450 2
6394_0452_0002 BLOCK1 interval rank target_tm:76.00;probe_tm:75.90;freq: 5.80;count:01;rules:0000;score:0871 chr14:1-83175860 TGAGTTGTATGGTATGTGAATTTCATCTCCAGAACACTTGTTAAAGTCCACTTGACAGATATGC 0 64469676 64469676 2 452 experimental CHR14FS062978463 62978463 6394 452 2
6394_0454_0002 BLOCK1 interval rank target_tm:76.00;probe_tm:75.80;freq: 2.35;count:01;rules:0000;score:0934 chr7:1-76062954 AGCAGCTGGCAAGAAGGCAAATGAGGGAGAGGCGTTAATGATAATATAGAT 0 64273149 64273149 2 454 experimental CHR07FS014598681 14598681 6394 454 2
6394_0456_0002 BLOCK1 interval rank target_tm:76.00;probe_tm:75.60;freq: 1.93;count:01;rules:0000;score:0944 chr7:1-76062954 GCATACCCTAACAAACTCAGTTGCTGAACACGTCTCTATTTCAACACTGTAAAAATGCTA 0 64272485 64272485 2 456 experimental CHR07FS014191585 14191585 6394 456 2
6394_0458_0002 BLOCK1 interval rank target_tm:76.00;probe_tm:75.50;freq: 2.38;count:01;rules:-400;score:0528 chr7:1-76062954 TATATGGGCCGCAGAAAGTTCCACCCCTTTTGGAGTTTGATTTTGAGTGATAAA 0 64265036 64265036 2 458 experimental CHR07FS009693703 9693703 6394 458 2
6394_0460_0002 BLOCK1 interval rank target_tm:76.00;probe_tm:75.90;freq: 2.44;count:01;rules:0000;score:0934 chr17:1-25535214 TAGGTCTTTGCCTGGCCAAAAGAGTAAGAATTAATACCTTTCTGCCTAAGAGTGTGA 0 64504632 64504632 2 460 experimental CHR17FS000891314 891314 6394 460 2
6394_0462_0002 BLOCK1 interval rank target_tm:76.00;probe_tm:75.80;freq: 3.05;count:01;rules:0000;score:0915 chr7:1-76062954 CAACTGGAAGTATGAGTCTGAAGTTTAGGAGAGGCTGGAGATGCATTTGAA 0 64291365 64291365 2 462 experimental CHR07FS026675445 26675445 6394 462 2
6394_0464_0002 BLOCK1 interval rank target_tm:76.00;probe_tm:75.60;freq: 1.92;count:01;rules:-400;score:0545 chr7:1-76062954 CCCAGGGGACCTGTTTCATTAGTCTGGAGTATATTATTTAGGCTGAGATAGAA 0 64305140 64305140 2 464 experimental CHR07FS035168547 35168547 6394 464 2
6394_0466_0002 BLOCK1 interval rank target_tm:76.00;probe_tm:75.60;freq:17.72;count:01;rules:0000;score:0785 chr17:1-25535214 TCTCTTGTAACCAATACTACTGGGATTAAAAATGGAAAGAAGGGAGGGAGGGA 0 64539990 64539990 2 466 experimental CHR17FS021757305 21757305 6394 466 2
6394_0468_0002 BLOCK1 interval rank target_tm:76.00;probe_tm:75.90;freq:23.83;count:01;rules:0000;score:0769 chr7:1-76062954 TAGAGGTTAAGGATTCTGCATTGTCACAGTTGTGGCTCAGGTTACTGCTT 0 64289833 64289833 2 468 experimental CHR07FS025458333 25458333 6394 468 2
6394_0470_0002 BLOCK1 interval rank target_tm:76.00;probe_tm:75.70;freq: 2.02;count:01;rules:0000;score:0943 chr4:1-52983990 GTTGAGAAAACGTATGGAAACTCAGGTGTACAATATGGTTTGTACAGTCTAGTCTGAGA 0 64228321 64228321 2 470 experimental CHR04FS040263214 40263214 6394 470 2
6394_0472_0002 BLOCK1 interval rank target_tm:76.00;probe_tm:75.90;freq: 2.33;count:01;rules:0000;score:0937 chr17:1-25535214 GACATGGATGCTGACAGCATCATTTTTGGAAGCTCATTCTACCTTGAGGA 0 64516849 64516849 2 472 experimental CHR17FS008078179 8078179 6394 472 2
6394_0474_0002 BLOCK1 interval rank target_tm:76.00;probe_tm:75.90;freq: 5.00;count:01;rules:-500;score:0382 chr7:1-76062954 AAAAAAAAAACAAGCTCACATTTTAAGCCATCAACTCAGGTCTACACAGCTGGCAGG 0 64276711 64276711 2 474 experimental CHR07FS017125604 17125604 6394 474 2
6394_0476_0002 BLOCK1 interval rank target_tm:76.00;probe_tm:75.90;freq: 4.64;count:01;rules:0000;score:0887 chr4:1-52983990 AACTTGTCCAGAGTCACAGAGCTGGTAAATTGCAGAGTGAGTGTCAAACT 0 64207874 64207874 2 476 experimental CHR04FS028590279 28590279 6394 476 2
6394_0478_0002 BLOCK1 interval rank target_tm:76.00;probe_tm:75.90;freq:25.81;count:01;rules:0000;score:0764 chr7:1-76062954 AGGTTTGCAACTTGCTGAGCCACAGCGGAAACTCCAACAGACTTTTAATT 0 64350616 64350616 2 478 experimental CHR07FS064469530 64469530 6394 478 2
6394_0480_0002 BLOCK1 interval rank target_tm:76.00;probe_tm:75.70;freq: 2.11;count:01;rules:0000;score:0940 chr14:1-83175860 AAAGTTTTCCAGGATGGTTTAGGATTCTGGGTGCCAAGAGCACATCCATAAA 0 64481831 64481831 2 480 experimental CHR14FS070446398 70446398 6394 480 2
6394_0482_0002 BLOCK1 interval rank target_tm:76.00;probe_tm:75.90;freq: 3.64;count:01;rules:-300;score:0605 chr17:1-25535214 AGCCCTGGTTTTTTCTCTTGCATCCTTTCTTTCAGGGACCTAAGTGTCTA 0 64511522 64511522 2 482 experimental CHR17FS005053371 5053371 6394 482 2
6394_0484_0002 BLOCK1 interval rank target_tm:76.00;probe_tm:75.70;freq: 1.61;count:01;rules:0000;score:0960 chr7:1-76062954 AGTTGAAAACGTTACTGTTTCACTCCTGGACTCTGCCAGTACTTGCCTAATT 0 64282226 64282226 2 484 experimental CHR07FS020505175 20505175 6394 484 2

Total number of rows: 392778

Table truncated, full table size 99444 Kbytes.




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Supplementary file Size Download File type/resource
GPL6553.pos.gz 2.7 Mb (ftp)(http) POS

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