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GEO help: Mouse over screen elements for information. |
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Status |
Public on Mar 06, 2009 |
Title |
NimbleGen/UWash Human 385K Design 2 |
Technology type |
in situ oligonucleotide |
Distribution |
custom-commercial |
Organism |
Homo sapiens |
Manufacturer |
NimbleGen custom 385K |
Manufacture protocol |
Manufactured by NimbleGen according to manufacturer's protocol.
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Contributor(s) |
Marques-Bonet T, Kidd JM, Ventura M, Graves TA, Cheng Z, Hillier LW, Jiang Z, Baker C, Malfavon-Borja R, Fulton LA, Alkan C, Aksay G, Girirajan S, Siswara P, Chen L, Cardone M, Navarro A, Mardis ER, Wilson RK, Eichler EE |
Submission date |
Dec 06, 2008 |
Last update date |
Mar 06, 2009 |
Contact name |
Tomas Marques-Bonet |
URL |
http://eichlerlab.gs.washington.edu/
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Organization name |
University of Washington
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Department |
Genome Sciences
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Lab |
Evan Eichler
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Street address |
1705 NE Pacific St,
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City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98195 |
Country |
USA |
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Samples (65)
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GSM348295, GSM349654, GSM349679, GSM349722, GSM349723, GSM349724
GSM349726, GSM758326, GSM758327, GSM758328, GSM758329, GSM758330, GSM758331, GSM758332, GSM758333, GSM758334, GSM758335, GSM758336, GSM758337, GSM758338, GSM758339, GSM758340, GSM758341, GSM758342, GSM758343, GSM758344, GSM758345, GSM758346, GSM758347, GSM758348, GSM758349, GSM758350, GSM758351, GSM758352, GSM758353, GSM758354, GSM758355, GSM758356, GSM758357, GSM758358, GSM758359, GSM758362, GSM758363, GSM758364, GSM758365, GSM758366, GSM758367, GSM758368, GSM758369, GSM758370, GSM758371, GSM758372, GSM758373, GSM758374, GSM758375, GSM758376, GSM758377, GSM758378, GSM758379, GSM758380, GSM758381, GSM758382, GSM758383, GSM758384, GSM758385
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Series (4)
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GSE13884 |
INTER_specific hybs: A Burst of Segmental Duplications in the African Great Ape Ancestor |
GSE13885 |
INTRA_specific hybs: A Burst of Segmental Duplications in the African Great Ape Ancestor |
GSE13934 |
A Burst of Segmental Duplications in the African Great Ape Ancestor |
GSE30559 |
Great Ape Copy Number Variation |
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Data table header descriptions |
ID |
|
PROBE_DESIGN_ID |
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CONTAINER |
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DESIGN_NOTE |
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SELECTION_CRITERIA |
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SEQ_ID |
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PROBE_SEQUENCE |
Oligonucleotide sequence |
MISMATCH |
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MATCH_INDEX |
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FEATURE_ID |
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ROW_NUM |
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COL_NUM |
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PROBE_CLASS |
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POSITION |
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DESIGN_ID |
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X |
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Y |
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chrm |
Chromosome location (hg17) |
RANGE_GB |
RefSeq accession.version for chromosome sequence |
SPOT_ID |
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RANGE_START |
Start position on chromosome sequence |
RANGE_END |
End position on chromosome sequence |
genome_build |
UCSC Build hg17, NCBI Build 35 |
RANGE_STRAND |
Strand of chromosome sequence |
Data table |
ID |
PROBE_DESIGN_ID |
CONTAINER |
DESIGN_NOTE |
SELECTION_CRITERIA |
SEQ_ID |
PROBE_SEQUENCE |
MISMATCH |
MATCH_INDEX |
FEATURE_ID |
ROW_NUM |
COL_NUM |
PROBE_CLASS |
POSITION |
DESIGN_ID |
X |
Y |
chrm |
RANGE_GB |
SPOT_ID |
RANGE_START |
RANGE_END |
genome_build |
RANGE_STRAND |
CHR17FS041802350 |
7054_0603_0001 |
BLOCK1 |
interval rank |
target_tm:76.00;probe_tm:75.70;freq:21.05;count:02;rules:0000;score:0674 |
chr17:41789000-41935000 |
ACAGGTAACCTGCTAGAGAATTCCTTCTTGTTCTGGATGAGTTTGGCCTTTT |
0 |
64477634 |
64477634 |
1 |
603 |
experimental |
41802350 |
7054 |
603 |
1 |
chr17 |
NC_000017.9 |
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41802350 |
41802401 |
hg17 |
+ |
CHR04RFS000600459 |
7054_0605_0001 |
BLOCK1 |
interval rank |
target_tm:76.00;probe_tm:75.70;freq:12.23;count:02;rules:0000;score:0713 |
chr4_random:577309-607859 |
CAAAATGAACTGAGAGCCACGAAAGTGTTCCTCTGTGAACCAGCA |
0 |
64251036 |
64251036 |
1 |
605 |
experimental |
600459 |
7054 |
605 |
1 |
chr4_random |
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chr4_random |
600459 |
600503 |
hg17 |
+ |
CHR09FS045620238 |
7054_0607_0001 |
BLOCK1 |
interval rank |
target_tm:76.00;probe_tm:78.40;freq:21.81;count:02;rules:0000;score:0630 |
chr9:44225893-45631216 |
TTCTGAGATTAGGCTGGTTTCTCCTCTTGGCCCTGGCCTACAGAC |
0 |
64340361 |
64340361 |
1 |
607 |
experimental |
45620238 |
7054 |
607 |
1 |
chr9 |
NC_000009.9 |
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45620238 |
45620282 |
hg17 |
+ |
CHR08FS042789960 |
7054_0609_0001 |
BLOCK1 |
interval rank |
target_tm:76.00;probe_tm:73.20;freq:27.78;count:01;rules:0000;score:0704 |
chr8:42696310-42850493 |
GGTTTTAGTCTCTTACTGTGCAGGAAAATCCCTGGTCCTTATACAAATATATTTA |
0 |
64312831 |
64312831 |
1 |
609 |
experimental |
42789960 |
7054 |
609 |
1 |
chr8 |
NC_000008.9 |
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42789960 |
42790014 |
hg17 |
+ |
CHR09RFS000186717 |
7054_0611_0001 |
BLOCK1 |
interval rank |
target_tm:76.00;probe_tm:74.50;freq:55.91;count:03;rules:0000;score:0480 |
chr9_random:170000-234436 |
GTCAGAATTGCTATTATTTAAAAGGCGAAAAATAACAGGTGCTGGTAAAGCTGTGGA |
0 |
64352742 |
64352742 |
1 |
611 |
experimental |
186717 |
7054 |
611 |
1 |
chr9_random |
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chr9_random |
186717 |
186773 |
hg17 |
+ |
CHR05FS075067070 |
7054_0613_0001 |
BLOCK1 |
interval rank |
target_tm:76.00;probe_tm:70.20;freq:33.66;count:01;rules:0000;score:0630 |
chr5:75000000-75100000 |
ATAAAGTCAATTTTCTATATTTTAGTGGGAGATTCAAAGACTCACATGATTTATACAA |
0 |
64260600 |
64260600 |
1 |
613 |
experimental |
75067070 |
7054 |
613 |
1 |
chr5 |
NC_000005.8 |
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75067070 |
75067127 |
hg17 |
+ |
CHR17FS034053850 |
7054_0615_0001 |
BLOCK1 |
interval rank |
target_tm:76.00;probe_tm:68.70;freq:82.58;count:01;rules:0000;score:0536 |
chr17:33267468-34078915 |
ATAATAATAATAACTAAAACAACAACAGGCTCATCAGAATGGTTAAAATTAAAG |
0 |
64475026 |
64475026 |
1 |
615 |
experimental |
34053850 |
7054 |
615 |
1 |
chr17 |
NC_000017.9 |
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34053850 |
34053903 |
hg17 |
+ |
CHR10FS015215280 |
7054_0617_0001 |
BLOCK1 |
interval rank |
target_tm:76.00;probe_tm:75.70;freq: 6.32;count:01;rules:0000;score:0861 |
chr10:14866084-15230896 |
CCACATAAAACCCTGTGGCAAAGAATACGGTTCTTGGCGTACGTT |
0 |
64355716 |
64355716 |
1 |
617 |
experimental |
15215280 |
7054 |
617 |
1 |
chr10 |
NC_000010.8 |
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15215280 |
15215324 |
hg17 |
+ |
CHR07FS142830250 |
7054_0619_0001 |
BLOCK1 |
interval rank |
target_tm:76.00;probe_tm:75.50;freq:18.05;count:02;rules:0000;score:0681 |
chr7:142805000-142868000 |
CCACTGGCTCCAAGACAACTGAAATCTTCAGGACAAAATCAAACTTTATGTCTG |
0 |
64299592 |
64299592 |
1 |
619 |
experimental |
142830250 |
7054 |
619 |
1 |
chr7 |
NC_000007.11 |
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142830250 |
142830303 |
hg17 |
+ |
CHR05FS069653463 |
7054_0621_0001 |
BLOCK1 |
interval rank |
target_tm:76.00;probe_tm:78.40;freq:17.55;count:09;rules:0000;score:-055 |
chr5:69604000-69672680 |
ACTCCTGGGTGAATGGCTGATCTGTCTCACTCTTCTCCGTGATCC |
0 |
64258888 |
64258888 |
1 |
621 |
experimental |
69653463 |
7054 |
621 |
1 |
chr5 |
NC_000005.8 |
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69653463 |
69653507 |
hg17 |
+ |
CHR11FS000078351 |
7054_0623_0001 |
BLOCK1 |
interval rank |
target_tm:76.00;probe_tm:75.70;freq:18.53;count:04;rules:0000;score:0483 |
chr11:45001-110000 |
ATATGTTTTGGAGGGATTTCACCAGAGTTTTTGCTAAGATGCATAAAATGGCCACAGAG |
0 |
64372883 |
64372883 |
1 |
623 |
experimental |
78351 |
7054 |
623 |
1 |
chr11 |
NC_000011.8 |
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78351 |
78409 |
hg17 |
+ |
CHR11FS115838855 |
7054_0625_0001 |
BLOCK1 |
interval rank |
target_tm:76.00;probe_tm:73.50;freq:24.94;count:01;rules:0000;score:0718 |
chr11:115830805-116041502 |
CTACTCTATGGAGTGCAGTACATAGAGACTTAATAAATACTTGACAAATGAAACAGTGAAT |
0 |
64387627 |
64387627 |
1 |
625 |
experimental |
115838855 |
7054 |
625 |
1 |
chr11 |
NC_000011.8 |
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115838855 |
115838915 |
hg17 |
+ |
CHR01FS000494929 |
7054_0627_0001 |
BLOCK1 |
interval rank |
target_tm:76.00;probe_tm:75.70;freq:27.68;count:05;rules:0000;score:0354 |
chr1:476479-497000 |
TCCACCCAATGCAAAAAGCATACTGCCTTCTCTTCTGCATTGGTG |
0 |
64160239 |
64160239 |
1 |
627 |
experimental |
494929 |
7054 |
627 |
1 |
chr1 |
NC_000001.8 |
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494929 |
494973 |
hg17 |
+ |
CHR03FS089688457 |
7054_0629_0001 |
BLOCK1 |
interval rank |
target_tm:76.00;probe_tm:74.40;freq:65.18;count:01;rules:0000;score:0667 |
chr3:89591682-89771786 |
GGAATACTATACAGCCGTAAAATAGGACAAGATTATGTCATTTGTAGGAACAAGGATG |
0 |
64218213 |
64218213 |
1 |
629 |
experimental |
89688457 |
7054 |
629 |
1 |
chr3 |
NC_000003.9 |
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89688457 |
89688514 |
hg17 |
+ |
CHR04FS107887356 |
7054_0631_0001 |
BLOCK1 |
interval rank |
target_tm:76.00;probe_tm:72.40;freq:33.29;count:01;rules:0000;score:0675 |
chr4:107874806-108081978 |
CTGTATTTAAGTGTCCGAGTGAGTTGTTTTCTTTTATACTTAATGAGTTTATGCTG |
0 |
64237032 |
64237032 |
1 |
631 |
experimental |
107887356 |
7054 |
631 |
1 |
chr4 |
NC_000004.9 |
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107887356 |
107887411 |
hg17 |
+ |
CHR20FS025962322 |
7054_0633_0001 |
BLOCK1 |
interval rank |
target_tm:76.00;probe_tm:75.80;freq:24.84;count:02;rules:0000;score:0664 |
chr20:25639533-26013217 |
CCATGCTTAGCTCCTTTCATCATTTCAAACTGAGCTTGGAGAAGAACCTGA |
0 |
64502999 |
64502999 |
1 |
633 |
experimental |
25962322 |
7054 |
633 |
1 |
chr20 |
NC_000020.9 |
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25962322 |
25962372 |
hg17 |
+ |
CHRXFS042629554 |
7054_0635_0001 |
BLOCK1 |
interval rank |
target_tm:76.00;probe_tm:76.60;freq:42.52;count:01;rules:0000;score:0718 |
chrX:42515252-42678922 |
AATCCCTTTCGCTTGGTTCGCATTCTCTCTGCCTGCTGCCATTTA |
0 |
64521805 |
64521805 |
1 |
635 |
experimental |
42629554 |
7054 |
635 |
1 |
chrX |
NC_000023.8 |
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42629554 |
42629598 |
hg17 |
+ |
CHR16FS015452853 |
7054_0637_0001 |
BLOCK1 |
interval rank |
target_tm:76.00;probe_tm:74.40;freq:47.11;count:01;rules:0000;score:0690 |
chr16:15451000-15482958 |
CGTTTGTTTTACTTATGCCTATGTGTGTATGTACATACTGGGTCACTCTTAGTATTTC |
0 |
64445333 |
64445333 |
1 |
637 |
experimental |
15452853 |
7054 |
637 |
1 |
chr16 |
NC_000016.8 |
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15452853 |
15452910 |
hg17 |
+ |
CHR17FS007288650 |
7054_0639_0001 |
BLOCK1 |
interval rank |
target_tm:76.00;probe_tm:75.30;freq:19.29;count:01;rules:-300;score:0472 |
chr17:7247848-7598744 |
CCAAAAAGGGCCTGTCTAGATTTTTTCAGAAAAACGTGGAGTGCTAGG |
0 |
64466063 |
64466063 |
1 |
639 |
experimental |
7288650 |
7054 |
639 |
1 |
chr17 |
NC_000017.9 |
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7288650 |
7288697 |
hg17 |
+ |
CHR15FS019173800 |
7054_0641_0001 |
BLOCK1 |
interval rank |
target_tm:76.00;probe_tm:70.90;freq:40.84;count:01;rules:0000;score:0630 |
chr15:19166000-19220000 |
AGATAAATTAACCATCATAGGAGAACATAAAACATAAATATCTAAGGGTGAACTAGA |
0 |
64422320 |
64422320 |
1 |
641 |
experimental |
19173800 |
7054 |
641 |
1 |
chr15 |
NC_000015.8 |
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19173800 |
19173856 |
hg17 |
+ |
Total number of rows: 385027
Table truncated, full table size 116449 Kbytes.
Supplementary file |
Size |
Download |
File type/resource |
GPL7749.ndf.gz |
27.7 Mb |
(ftp)(http) |
NDF |
GPL7749.pos.gz |
3.1 Mb |
(ftp)(http) |
POS |
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