NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Platform GPL9684 Query DataSets for GPL9684
Status Public on Feb 18, 2010
Title Eichler-NimbleGen Human 2.1 HD2 CGH chip
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Homo sapiens
Manufacturer NimbleGen
Manufacture protocol 2.1 Million genome wide CGH chip based on UCSC hg18
 
 
Contributor(s) Alkan C, Kidd JM, Eichler EE
Submission date Nov 16, 2009
Last update date Oct 27, 2010
Contact name Jeffrey M Kidd
E-mail(s) kiddj@u.washington.edu
Phone 2066857336
Fax 2062215795
Organization name University of Washington
Department Department of Genome Sciences
Lab Eichler Lab
Street address 1705 NE Pacific St
City Seattle
State/province WA
ZIP/Postal code 98195-5065
Country USA
 
Samples (3) GSM471434, GSM667894, GSM668114
Series (2)
GSE19048 Complete Genomes of a Hunter-Gatherer and a Bantu from Southern Africa
GSE27072 Structural variation of the gorilla genome

Data table header descriptions
ID
PROBE_DESIGN_ID probe id
CONTAINER
DESIGN_NOTE
SELECTION_CRITERIA
SEQ_ID
SEQUENCE
MISMATCH
MATCH_INDEX
FEATURE_ID
ROW_NUM
COL_NUM
PROBE_CLASS
POSITION
DESIGN_ID
X
Y
DMD
CHROMOSOME probe chromosome
RANGE_GB GenBank Accession number
RANGE_START probe begin
RANGE_END probe end
genome_build genome assembly version
RANGE_STRAND probe strand

Data table
ID PROBE_DESIGN_ID CONTAINER DESIGN_NOTE SELECTION_CRITERIA SEQ_ID SEQUENCE MISMATCH MATCH_INDEX FEATURE_ID ROW_NUM COL_NUM PROBE_CLASS POSITION DESIGN_ID X Y DMD CHROMOSOME RANGE_GB RANGE_START RANGE_END genome_build RANGE_STRAND
CHR14P030552598 5058_1_1 FORWARD interval rank target_tm:76.00;probe_tm:75.30;freq:75.00;count:01;rules:0000;score:0675 chr14:1-106368585 TGAAGAGCAGTGGTGTGATGATAGCTCATTACAACTTCAAACTCCTGG 0 172977116 172977116 1 1 experimental 30552598 5058 1 1 A03 chr14 NC_000014.7 30552598 30552645 hg18 +
CHRYP026597055 5058_1_3 FORWARD interval rank target_tm:76.00;probe_tm:75.00;freq:13.24;count:04;rules:0000;score:0494 chrY:1-57772954 TATGGGAAAGGTTGAGCCCATGGATGTTAACTGGCATATATTAAAGGATAAGGACATAA 0 173532772 173532772 3 1 experimental 26597055 5058 1 3 A03 chrY NC_000024.8 26597055 26597113 hg18 +
CHR14P033961542 5058_1_5 FORWARD interval rank target_tm:76.00;probe_tm:69.50;freq:25.63;count:01;rules:0000;score:0636 chr14:1-106368585 TGTAAACCACTTGCACATAATAGTTCTCAACAATAAGTAATTATTACAATATTAATATGA 0 172979732 172979732 5 1 experimental 33961542 5058 1 5 A03 chr14 NC_000014.7 33961542 33961601 hg18 +
CHR20P030592238 5058_1_7 FORWARD interval rank target_tm:76.00;probe_tm:75.70;freq: 7.74;count:01;rules:0000;score:0846 chr20:1-62435964 ATCTAAGTAAGGCTATCCTGGTTAGCCAAAAGCATCCCATGCCCA 0 173329646 173329646 7 1 experimental 30592238 5058 1 7 A03 chr20 NC_000020.9 30592238 30592282 hg18 +
CHR14P036440864 5058_1_9 FORWARD interval rank target_tm:76.00;probe_tm:76.00;freq:11.10;count:01;rules:0000;score:0826 chr14:1-106368585 AATCTTCTATGCACTGTGTATGACAAACATTCAAGTCCCATGAACTCCAAGGTCATCCATTTA 0 172981517 172981517 9 1 experimental 36440864 5058 1 9 A03 chr14 NC_000014.7 36440864 36440926 hg18 +
CHR20P042469034 5058_1_11 FORWARD interval rank target_tm:76.00;probe_tm:77.50;freq: 6.39;count:01;rules:0000;score:0836 chr20:1-62435964 CCCTCCAGAGAGAGGCTTATGTGAACCGAGTATTAACTCTGAGCC 0 173338550 173338550 11 1 experimental 42469034 5058 1 11 A03 chr20 NC_000020.9 42469034 42469078 hg18 +
CHR15P071066789 5058_1_13 FORWARD interval rank target_tm:76.00;probe_tm:75.60;freq:34.84;count:01;rules:0000;score:0736 chr15:1-100338915 GGGTAAACTAGATGGCCACCTGCAGAATAAAATTGGACCCTGATCT 0 173075023 173075023 13 1 experimental 71066789 5058 1 13 A03 chr15 NC_000015.8 71066789 71066834 hg18 +
CHR13P025228746 5058_1_15 FORWARD interval rank target_tm:76.00;probe_tm:77.50;freq: 6.13;count:01;rules:0000;score:0839 chr13:1-114142980 TAGGTTGTGACCTCGGGCATACTGTGTCAATCTTTCTGAGCTGGG 0 172897356 172897356 15 1 experimental 25228746 5058 1 15 A03 chr13 NC_000013.9 25228746 25228790 hg18 +
CHR13P034251970 5058_1_17 FORWARD interval rank target_tm:76.00;probe_tm:75.50;freq:13.76;count:01;rules:0000;score:0801 chr13:1-114142980 CAGGAAAGACACCTTTCCCTCCTGAATGTGGAAATCTACAAGTCCAT 0 172904504 172904504 17 1 experimental 34251970 5058 1 17 A03 chr13 NC_000013.9 34251970 34252016 hg18 +
CHR16P072161193 5058_1_19 FORWARD interval rank target_tm:76.00;probe_tm:76.60;freq:11.81;count:01;rules:0000;score:0810 chr16:1-88827254 ATGCCAGGATGGAGCTCAAGAACAGTTAATCCCACAAGGAACCCA 0 173142313 173142313 19 1 experimental 72161193 5058 1 19 A03 chr16 NC_000016.8 72161193 72161237 hg18 +
CHRXP080921642 5058_1_21 FORWARD interval rank target_tm:76.00;probe_tm:74.40;freq:14.43;count:01;rules:0000;score:0775 chrX:1-154913754 AGGTTCAGCACCAGCTTGTGAATTATGTTATTAACAACTCAAATTCTACTGGTCTTTG 0 173461593 173461593 21 1 experimental 80921642 5058 1 21 A03 chrX NC_000023.9 80921642 80921699 hg18 +
CHR19P060445203 5058_1_23 FORWARD interval rank target_tm:76.00;probe_tm:83.90;freq:22.94;count:01;rules:0000;score:0616 chr19:1-63811651 CACTGTGCAGGGAGCACAGGCAGCCACAGAGCAAGGTGCCACGGG 0 173305610 173305610 23 1 experimental 60445203 5058 1 23 A03 chr19 NC_000019.8 60445203 60445247 hg18 +
CHR14P036535465 5058_1_25 FORWARD interval rank target_tm:76.00;probe_tm:75.30;freq:11.22;count:01;rules:0000;score:0812 chr14:1-106368585 AATGTGTTCTTGTGAGCAGAAAAGTAAGCTGTTGATTAAGCACATTGACTTGCTACATTCTGT 0 172981598 172981598 25 1 experimental 36535465 5058 1 25 A03 chr14 NC_000014.7 36535465 36535527 hg18 +
CHR15P026740105 5058_1_27 FORWARD interval rank target_tm:76.00;probe_tm:70.20;freq:49.58;count:03;rules:0000;score:0402 chr15:1-100338915 ATGAATGAAAAATTGTTGATGATGTATGTATGTAGGGCAGTTATATTATTTTTCTTAAC 0 173041002 173041002 27 1 experimental 26740105 5058 1 27 A03 chr15 NC_000015.8 26740105 26740163 hg18 +
CHRYP005929152 5058_1_29 FORWARD interval rank target_tm:76.00;probe_tm:75.80;freq:18.45;count:02;rules:0000;score:0686 chrY:1-57772954 TAGGGACATCATATCACTTTTCCTGGCCTCATCTGTTAAACACCATTACACATCTATTCATATCA 0 173519951 173519951 29 1 experimental 5929152 5058 1 29 A03 chrY NC_000024.8 5929152 5929216 hg18 +
CHR12P030224909 5058_1_31 FORWARD interval rank target_tm:76.00;probe_tm:74.50;freq:16.02;count:01;rules:0000;score:0770 chr12:1-132349534 GAAACACATTACTTGAATTTCCTATGTGACCAGGAAATCCACACATTTTTCAGTAGG 0 172816009 172816009 31 1 experimental 30224909 5058 1 31 A03 chr12 NC_000012.10 30224909 30224965 hg18 +
CHR21P039673908 5058_1_33 FORWARD interval rank target_tm:76.00;probe_tm:76.60;freq: 7.65;count:01;rules:0000;score:0841 chr21:1-46944323 AACACGGACGTCAGAAAACTGGTTCAGTAGGGATGGGTGCTAGAA 0 173375128 173375128 33 1 experimental 39673908 5058 1 33 A03 chr21 NC_000021.7 39673908 39673952 hg18 +
CHRXP141364452 5058_1_35 FORWARD interval rank target_tm:76.00;probe_tm:75.40;freq: 7.32;count:01;rules:0000;score:0844 chrX:1-154913754 CTCATCCTGTATACCTGGCTGGACTTTAATAATCGGTTATGAGCTTTTCCCTTTT 0 173505907 173505907 35 1 experimental 141364452 5058 1 35 A03 chrX NC_000023.9 141364452 141364506 hg18 +
CHR19P007726589 5058_1_37 FORWARD interval rank target_tm:76.00;probe_tm:72.40;freq:70.07;count:01;rules:0000;score:0621 chr19:1-63811651 ACTCCTGCTCACTTTTTGTTTCCATTTGTTAGAATTTCTTTTATCATCCTTTCAC 0 173276164 173276164 37 1 experimental 7726589 5058 1 37 A03 chr19 NC_000019.8 7726589 7726643 hg18 +
CHR21P046851447 5058_1_39 FORWARD interval rank target_tm:76.00;probe_tm:75.50;freq: 8.09;count:01;rules:0000;score:0839 chr21:1-46944323 GTGAGTGGAACACCTGAAAAGTTCCATGGTCTGTAGCCTACATATGA 0 173380724 173380724 39 1 experimental 46851447 5058 1 39 A03 chr21 NC_000021.7 46851447 46851493 hg18 +

Total number of rows: 2175072

Table truncated, full table size 658673 Kbytes.




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

Supplementary file Size Download File type/resource
GPL9684_HG18_CGH_LISOv1_HX1.ndf.gz 131.3 Mb (ftp)(http) NDF
GPL9684_HG18_CGH_LISOv1_HX1.pos.gz 16.6 Mb (ftp)(http) POS

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