NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Platform GPL7748 Query DataSets for GPL7748
Status Public on Mar 06, 2009
Title NimbleGen/UWash Human 385K Design 1
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.
 
Description This design was targeted to the "union" human regions (B35) that have at least one segmental duplication in any primate species analyzed (human, chimp, orang and macaque).
 
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 (40) GSM348287, GSM348288, GSM348289, GSM348290, GSM348291, GSM348292 
Series (3)
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
CHR15FS028317785 5834_0522_0282 SD interval rank target_tm:76.00;probe_tm:73.30;freq:29.49;count:02;rules:0000;score:0602 chr15:28152000-28935771 TTTTTGGTGTGCAACATGATGATTTGACATATGTATGCATTGTGTAGTGATTACCAAAATCAAAT 0 63986384 63986384 282 522 experimental 28317785 5834 522 282 chr15 NC_000015.8 28317785 28317849 hg17 +
CHR08FS086900910 5834_0524_0282 SD interval rank target_tm:76.00;probe_tm:75.90;freq:19.09;count:09;rules:0000;score:-015 chr8:86851003-86915143 TCCTAAAATTGTCTGCAGTGCAAATGGATTATGTGCATCCAACAGGAAACAGCATAG 0 63901062 63901062 282 524 experimental 86900910 5834 524 282 chr8 NC_000008.9 86900910 86900966 hg17 +
CHR06FS033643300 5834_0526_0282 Flank/Control interval rank target_tm:76.00;probe_tm:83.30;freq: 5.03;count:01;rules:0000;score:0738 chr6:33642000-33647000 CAGCTAAGGAGTGACCGTCTACAGGAGCGGCCTCTGACTCAGGGTGGCCA 0 63401255 63401255 282 526 experimental 33643300 5834 526 282 chr6 NC_000006.9 33643300 33643349 hg17 +
CHR17FS022449056 5834_0528_0282 SD interval rank target_tm:76.00;probe_tm:75.70;freq:13.54;count:01;rules:0000;score:0806 chr17:22438239-22496944 CATTCTCTTGGAGAACATTCTGGCAGTAAAGTAATAGATACATTGCATCCATCATTGTGTGTCAAA 0 64021228 64021228 282 528 experimental 22449056 5834 528 282 chr17 NC_000017.9 22449056 22449121 hg17 +
CHRXRFS001482900 5834_0530_0282 Flank/Control interval rank target_tm:76.00;probe_tm:69.40;freq:35.20;count:04;rules:0000;score:0311 chrX_random:1479000-1484000 TCATTTATAAAGTTGTTCTTATGAGAAAACATGTTTCATCTTCAAAATTGAGAAACAA 0 63448451 63448451 282 530 experimental 1482900 5834 530 282 chrX_random chrX_random 1482900 1482957 hg17 +
CHR10FS046628259 5834_0532_0282 SD interval rank target_tm:76.00;probe_tm:76.80;freq:13.94;count:10;rules:0000;score:-106 chr10:46480000-46849175 AACTACGTCCTGACCAGACACCTATCTCTAGATGCAACAGAATCCCTGTA 0 63936037 63936037 282 532 experimental 46628259 5834 532 282 chr10 NC_000010.8 46628259 46628308 hg17 +
CHR16FS018700766 5834_0534_0282 SD interval rank target_tm:76.00;probe_tm:80.00;freq: 7.08;count:02;rules:0000;score:0679 chr16:18061000-18702003 GTGATCAACAGTGCCCATTGCACTTCAATGGGCACCTGCAAGTGGCACCA 0 64001866 64001866 282 534 experimental 18700766 5834 534 282 chr16 NC_000016.8 18700766 18700815 hg17 +
CHR14FS019206985 5834_0536_0282 SD interval rank target_tm:76.00;probe_tm:78.40;freq: 9.78;count:03;rules:0000;score:0588 chr14:18070000-19402428 TTGGGAGAACAGCCTCGGTTTTTGCACTCGTGGTGGTGTGTATTTTGGGA 0 63974055 63974055 282 536 experimental 19206985 5834 536 282 chr14 NC_000014.7 19206985 19207034 hg17 +
CHR05FS027850307 5834_0538_0282 SD interval rank target_tm:76.00;probe_tm:75.90;freq:15.00;count:01;rules:0000;score:0803 chr5:27818330-27864530 TCAAGGAGCAATTATATGTACATGGAAATGTTCCTCTAGGTGAGAGAATGGTGCTGT 0 63839861 63839861 282 538 experimental 27850307 5834 538 282 chr5 NC_000005.8 27850307 27850363 hg17 +
CHR07FS062345284 5834_0540_0282 SD interval rank target_tm:76.00;probe_tm:75.70;freq:15.13;count:03;rules:0000;score:0598 chr7:62283000-62756852 ATTCTGTACTCACCTAATTCTGTCAGCCACAGCCATTAGCAAAAAGTGCAAG 0 63874780 63874780 282 540 experimental 62345284 5834 540 282 chr7 NC_000007.11 62345284 62345335 hg17 +
CHR08FS001344138 5834_0542_0282 SD interval rank target_tm:76.00;probe_tm:76.80;freq: 9.50;count:01;rules:0000;score:0822 chr8:1316000-1347023 ACACACGGTGTTAACTGTTCGGCAACTGGAGTTTCTAAGCCTGTTTTCTG 0 63892769 63892769 282 542 experimental 1344138 5834 542 282 chr8 NC_000008.9 1344138 1344187 hg17 +
CHR10FS127574235 5834_0544_0282 SD interval rank target_tm:76.00;probe_tm:79.20;freq: 1.53;count:01;rules:0000;score:0905 chr10:127561000-127611291 CAAAACGTGTGGGCAGATTCCGTAACTCAACCGGAAACGCGAAGGACTGA 0 63944804 63944804 282 544 experimental 127574235 5834 544 282 chr10 NC_000010.8 127574235 127574284 hg17 +
CHR03FS140787100 5834_0546_0282 SD interval rank target_tm:76.00;probe_tm:74.60;freq:13.88;count:01;rules:0000;score:0782 chr3:140756000-140788264 TATTTGTGAAAGATCCTCCAGATCTAAGATAGATATTCCAGAGACACTTCATATTTGCTTTTGC 0 63822598 63822598 282 546 experimental 140787100 5834 546 282 chr3 NC_000003.9 140787100 140787163 hg17 +
CHR01FS158216901 5834_0548_0282 SD interval rank target_tm:76.00;probe_tm:77.60;freq:57.69;count:11;rules:0000;score:-325 chr1:158212000-158267780 GCCACTTTGACCCAACCACTTTGACACAACCTGGAGCTCACAAAAACATG 0 63788771 63788771 282 548 experimental 158216901 5834 548 282 chr1 NC_000001.8 158216901 158216950 hg17 +
CHR03FS048731000 5834_0550_0282 SD interval rank target_tm:76.00;probe_tm:76.80;freq:13.31;count:01;rules:0000;score:0797 chr3:48731000-48748545 ATCTATATTCAGTGCACCAGGAAGGTCTGCTGTCTCCATCAGCATCATCT 0 63818014 63818014 282 550 experimental 48731000 5834 550 282 chr3 NC_000003.9 48731000 48731049 hg17 +
CHR16FS018215628 5834_0552_0282 SD interval rank target_tm:76.00;probe_tm:75.80;freq:21.96;count:03;rules:0000;score:0573 chr16:18061000-18702003 CCAGCAGATGACAGGCTAGGATAATTGATCATTAGAACATCTGTGCTGTTTTTGTTGTAAGAATA 0 64001013 64001013 282 552 experimental 18215628 5834 552 282 chr16 NC_000016.8 18215628 18215692 hg17 +
CHR17FS063785760 5834_0556_0282 Flank/Control interval rank target_tm:76.00;probe_tm:76.80;freq: 5.06;count:01;rules:0000;score:0867 chr17:63781354-63786354 ACCAAGGTAGCCAAATTAAAAGGGCCCTATACTTACGTCATGGTTAGGCC 0 63434252 63434252 282 556 experimental 63785760 5834 556 282 chr17 NC_000017.9 63785760 63785809 hg17 +
CHR06FS090403801 5834_0558_0282 SD interval rank target_tm:76.00;probe_tm:71.00;freq: 9.13;count:01;rules:0000;score:0740 chr6:90392000-90407512 ATAAAGTGAAATCTGGTTATAGTTTTACCTGGTTAAACAAGGTATAGCTATAC 0 63862197 63862197 282 558 experimental 90403801 5834 558 282 chr6 NC_000006.9 90403801 90403853 hg17 +
CHR05FS027836595 5834_0560_0282 SD interval rank target_tm:76.00;probe_tm:75.80;freq: 8.22;count:01;rules:0000;score:0844 chr5:27818330-27864530 ATAATTGGCCAAACCAGCGAGGTAGCTTCTATTTGGCCAGTACGTTTCTTT 0 63839836 63839836 282 560 experimental 27836595 5834 560 282 chr5 NC_000005.8 27836595 27836645 hg17 +
CHR07FS057295889 5834_0562_0282 SD interval rank target_tm:76.00;probe_tm:81.70;freq: 5.39;count:01;rules:0000;score:0765 chr7:57277336-57302599 GGAGCAGAACTGACTCCTTACCCAGGAGGCGACCGAGAAGAGTGAGTGCA 0 63872624 63872624 282 562 experimental 57295889 5834 562 282 chr7 NC_000007.11 57295889 57295938 hg17 +

Total number of rows: 385283

Table truncated, full table size 116460 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp

Supplementary file Size Download File type/resource
GPL7748.ndf.gz 27.9 Mb (ftp)(http) NDF
GPL7748.pos.gz 3.2 Mb (ftp)(http) POS

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap