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Platform GPL7749 Query DataSets for GPL7749
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.
 
 
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/
Organization name University of Washington
Department Genome Sciences
Lab Evan Eichler
Street address 1705 NE Pacific St,
City Seattle
State/province WA
ZIP/Postal code 98195
Country USA
 
Samples (65) GSM348295, GSM349654, GSM349679, GSM349722, GSM349723, GSM349724 
Series (4)
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

Data table header descriptions
ID
PROBE_DESIGN_ID
CONTAINER
DESIGN_NOTE
SELECTION_CRITERIA
SEQ_ID
PROBE_SEQUENCE Oligonucleotide sequence
MISMATCH
MATCH_INDEX
FEATURE_ID
ROW_NUM
COL_NUM
PROBE_CLASS
POSITION
DESIGN_ID
X
Y
chrm Chromosome location (hg17)
RANGE_GB RefSeq accession.version for chromosome sequence
SPOT_ID
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 19173800 19173856 hg17 +

Total number of rows: 385027

Table truncated, full table size 116449 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
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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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