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Platform GPL7737 Query DataSets for GPL7737
Status Public on Dec 12, 2008
Title WiCell 2006-07-27 HG18 WG CGH
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Homo sapiens
Manufacturer NimbleGen
Manufacture protocol Single array CGH design for whole human genome (hg18; NCBI Build 36). Probes selected from hg18_tiling database using 6000 bp interval and 250 bp window. Isothermal probes with min length of 50 bp and max length of 75 bp and target Tm of 76C. Cycle restricted to 148 synthesis cycles. Interval spacing: 6253 bp (mean); 6270 bp (median). 3553 random probes added. Includes pseudo-autosomal regions from chrX and chrY, though the counts for those regions have been changed to 1 to allow standard analysis.
 
 
Contributor(s) Montgomery K, Patterson M
Submission date Dec 04, 2008
Last update date Dec 04, 2009
Contact name Melodee Patterson
E-mail(s) wicell@short-termsolutions.com
Phone 608-219-3274
Organization name WiCell
Street address 510 Charmany Dr Ste 58 & 59
City Madison
State/province WI
ZIP/Postal code 53719
Country USA
 
Samples (16) GSM234781, GSM234789, GSM234891, GSM237067, GSM242876, GSM258791 
Series (2)
GSE9313 Comparative genomic hybridization of human embryonic stem cell lines deposited in the National Stem Cell Bank
GSE12119 Human Embryonic Stem Cell Sublines

Data table header descriptions
ID
CHROMOSOME Human Chromosome
START The start position of the probes
END The end position of the probes
SEQUENCE The sequence of the probes
DESCRIPTION Characteristics of the probes
GB_RANGE Accession.version[start..end]
SPOT_ID

Data table
ID CHROMOSOME START END SEQUENCE DESCRIPTION GB_RANGE SPOT_ID
CHR17P004612721 chr17 4612721 4612771 GAATCCTGATATTGTTGTTCCACCATCTCTAAGGGTTGTCCTCACCAAAGA target_tm:76.00;probe_tm:75.80;freq: 7.30;count:01;rules:0000;score:0853 NC_000017.9[4612721..4612771]
CHR04P186800100 chr4 186800100 186800156 GGTTATCGAGATTCCACTAAGTATTCTCAGTGAGGCATGTGCTTTCTATACGTTGTT target_tm:76.00;probe_tm:75.90;freq: 8.19;count:01;rules:0000;score:0846 NC_000004.10[186800100..186800156]
CHR08P136656388 chr8 136656388 136656446 CAGTTCAGACCCTTGATTAGTTTGAGTGCTAATTGTCAGGTAGATGTTAAGCTAGTAAG target_tm:76.00;probe_tm:75.70;freq: 5.31;count:01;rules:0000;score:0874 NC_000008.9[136656388..136656446]
CHR06P028418836 chr6 28418836 28418885 AAATAAAGTTCTGGCCCAGATAAGGCTCATAGTGGGTCCACAGACACTCT target_tm:76.00;probe_tm:76.80;freq: 8.31;count:01;rules:0000;score:0831 NC_000006.10[28418836..28418885]
CHRXP050300083 chrX 50300083 50300138 AAAGGAATTAAACTGTTACACGAGGCATATTCACTTAGTGCAAAACAAAGCATTAA target_tm:76.00;probe_tm:72.40;freq:12.67;count:01;rules:0000;score:0745 NC_000023.9[50300083..50300138]
CHR01P001837746 chr1 1837746 1837795 CGCCTGTCGGCTGAGCAGATCAAGGAGTACAAGGGAGTCTTTGAGATGTT target_tm:76.00;probe_tm:79.20;freq: 6.25;count:01;rules:0000;score:0804 NC_000001.9[1837746..1837795]
CHR02P190681443 chr2 190681443 190681495 TGTTTGCAAAGACCGCAAGCTATTGTCTATGATTTGCCTGGGAATTATCCTTG target_tm:76.00;probe_tm:75.60;freq: 7.92;count:01;rules:0000;score:0843 NC_000002.10[190681443..190681495]
CHR03P076537568 chr3 76537568 76537626 TAATGTCAAAAGCAACCTTGAAAAGGAAAGCACTCATATAAGTAGCTGATGGGAATGGG target_tm:76.00;probe_tm:75.70;freq:17.27;count:01;rules:0000;score:0789 NC_000003.10[76537568..76537626]
CHR07P026443987 chr7 26443987 26444036 GGATGATTAAATCCAACTGGCACCGGACCTTGGGAGAGCCAATCCATTGT target_tm:76.00;probe_tm:78.40;freq: 5.69;count:01;rules:0000;score:0827 NC_000007.12[26443987..26444036]
CHR09P106637733 chr9 106637733 106637782 GCTTAAAGTAAAGGTCCTCAGCTTGACACACAAGTCCCTCCAAGGCATGC target_tm:76.00;probe_tm:78.40;freq: 7.42;count:01;rules:0000;score:0807 NC_000009.10[106637733..106637782]
CHR01P227262528 chr1 227262528 227262589 TACAGTTTTTCCCAGTGCTACTATGATAATCATCATGGCCTGATGAAGGTTAGAGTTCTAAT target_tm:76.00;probe_tm:75.40;freq: 8.21;count:01;rules:0000;score:0836 NC_000001.9[227262528..227262589]
CHR03P102656407 chr3 102656407 102656458 TCTTTTGGAGCATGATGGGATGTTCTAAAACCATCACCAGACTGTAGTGATG target_tm:76.00;probe_tm:75.70;freq:10.53;count:01;rules:0000;score:0824 NC_000003.10[102656407..102656458]
CHR14P057343980 chr14 57343980 57344029 GGGAAGTTTTGTTCCAACAGGGCTGTAGCAAAACACTATACTTGCTCTCA target_tm:76.00;probe_tm:75.90;freq: 8.69;count:01;rules:0000;score:0842 NC_000014.7[57343980..57344029]
CHR20P054706373 chr20 54706373 54706423 TTGTTGATAAATGTTTCGTGTTCAGGACACCTGAACACGAAACAGCAGGCA target_tm:76.00;probe_tm:75.80;freq: 6.59;count:01;rules:0000;score:0860 NC_000020.9[54706373..54706423]
CHR06P153050243 chr6 153050243 153050297 TTTTTAAGTCAAACAAGAGTATCTAGAGTTTCATTTCCAAGCACTTTATAATAAA target_tm:76.00;probe_tm:69.40;freq:16.83;count:01;rules:0000;score:0664 NC_000006.10[153050243..153050297]
CHRXP024343762 chrX 24343762 24343811 TTAGTGGCATTCACATGGTGCTAATTCTGAGGTGCGCAGAGTTTGAGAAC target_tm:76.00;probe_tm:76.80;freq:10.19;count:01;rules:0000;score:0817 NC_000023.9[24343762..24343811]
CHR02P191618921 chr2 191618921 191618970 TTCTTTGGTTGCGCTTGAGACGGACTAGTTGTCTTGAGTATAGGCACCAA target_tm:76.00;probe_tm:76.80;freq: 2.81;count:01;rules:0000;score:0910 NC_000002.10[191618921..191618970]
CHR03P178650190 chr3 178650190 178650247 AGTTTCCTTTTGACTCAATGTGGCAGTTGGACATAGCTGGATGTCTAAGTTTTCTTTC target_tm:76.00;probe_tm:75.80;freq:10.80;count:01;rules:0000;score:0824 NC_000003.10[178650190..178650247]
CHRXP056412666 chrX 56412666 56412724 TGAGGATCTCAGATGTGCTATCAGGACCTTGGATACTGAATATAGACTGGCATATATAA target_tm:76.00;probe_tm:75.70;freq: 7.22;count:01;rules:0000;score:0851 NC_000023.9[56412666..56412724]
CHRXP108181417 chrX 108181417 108181477 CTGCTATGCTAGTTGAAGATGTGGTGAATTTACATAAGTTCCTGTCCATTTCTAGTCCCAA target_tm:76.00;probe_tm:76.20;freq: 9.91;count:01;rules:0000;score:0831 NC_000023.9[108181417..108181477]

Total number of rows: 390934

Table truncated, full table size 76772 Kbytes.




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

Supplementary file Size Download File type/resource
GPL7737_2006_07_27_HG18_WG_CGH.ndf.gz 21.0 Mb (ftp)(http) NDF

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