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Sample GSM123893 Query DataSets for GSM123893
Status Public on Dec 06, 2006
Title S6
Sample type genomic
 
Channel 1
Source name S6-NA15760
Organism Homo sapiens
Characteristics B-lymphocyte cell line DNA
Biomaterial provider Coriell Cell Repositories
http://locus.umdnj.edu/nigms/nigms_cgi/display.cgi?NA15760
Coriell
Extracted molecule genomic DNA
Label Cyanine 3
 
Channel 2
Source name Mref
Organism Homo sapiens
Characteristics single male reference genomic DNA
Biomaterial provider anonymous normal male donor
Coriell
Extracted molecule genomic DNA
Label Cyanine 5
 
 
Description cyanine 3 = sample
cyanine 5 = reference
Data processing three-step normalization procedure; (Khojasteh et al BMC Bioinformatics 2005;6:274)
 
Submission date Jul 28, 2006
Last update date Dec 06, 2006
Contact name Kendy Wong
E-mail(s) kwong@bccrc.ca
Phone 604-675-8000
Organization name BC Cancer Research Center
Department Cancer Genetics
Lab Wan Lam Lab
Street address 675 West 10th Avenue
City Vancouver
State/province British Columbia
ZIP/Postal code V5Z 1L3
Country Canada
 
Platform ID GPL2616
Series (1)
GSE5442 A comprehensive analysis of copy number variations in the human genome

Data table header descriptions
ID_REF
Spot Mean Intensity (w595) Mean Spot Pixel Intensity - Cy3 channel
Spot Mean Intensity (w685) Mean Spot Pixel Intensity - Cy5 channel
Background Median Intensity (w595) Median Background Pixel Intensity - Cy3 channel
Background Median Intensity (w685) Median Background Pixel Intensity - Cy5 channel
Spot Normalized Intensity (w595) Spot Mean - Background Median
Spot Normalized Intensity (w685) Spot Mean - Background Median
Spot SNR (w595) Signal to noise ratio - Cy3
Spot SNR (w685) Signal to noise ratio - Cy5
Spot Ratio (w595) Cy3/Cy5
Spot Ratio (w685) Cy5/Cy3
Spot Log2 Ratio (w595) log2(Cy3/Cy5) (global mean set to 0)
VALUE normalized log2 (Cy3/Cy5; sample/ref)

Data table
ID_REF Spot Mean Intensity (w595) Spot Mean Intensity (w685) Background Median Intensity (w595) Background Median Intensity (w685) Spot Normalized Intensity (w595) Spot Normalized Intensity (w685) Spot SNR (w595) Spot SNR (w685) Spot Ratio (w595) Spot Ratio (w685) Spot Log2 Ratio (w595) VALUE
1 2836.918 2433.347 726 1866.5 2110.918 566.847 59.1924 14.47603 1.5439 0.6476867 0.6265791 0.444467
2 2958.465 2378.709 731 1837 2227.465 541.709 61.1486 14.62858 1.70474 0.5865782 0.7695517 0.562334
3 2483.586 2282.77 735 1846 1748.586 436.77 72.0829 13.35638 1.659769 0.6024714 0.7309825 0.520488
4 2673.286 2328.209 740 1864.5 1933.286 463.709 82.7869 16.14448 1.728479 0.578522 0.7895033 0.579556
5 2595.433 2367.2 750 1864 1845.433 503.2 100.2171 15.92803 1.520447 0.6576773 0.6044953 0.396905
6 3095.6 2475.21 744 1859 2351.6 616.21 107.1586 21.45439 1.582152 0.6320273 0.6618882 0.45955
7 3202.63 2552.917 757.5 1872 2445.129 680.917 103.7644 19.24034 1.488746 0.6716815 0.5740981 0.378847
8 2851.871 2458.021 751 1886 2100.871 572.021 26.46069 12.03597 1.522651 0.6567251 0.6065856 0.40832
9 4891.91 2948.932 756 1885 4135.91 1063.932 150.2874 32.0796 1.611652 0.6204585 0.6885403 0.507852
10 3409.51 2783.67 763.5 1881 2646.006 902.67 107.8635 27.40486 1.215276 0.822828 0.2812843 0.128467
11 3116.065 2687.293 766 1883 2350.065 804.293 71.0618 18.50432 1.211376 0.8254775 0.2766462 0.122741
12 3129.859 2753.152 777 1882 2352.859 871.152 64.9787 19.08012 1.119735 0.8930356 0.1631576 0.011704
13 3898.13 3109.674 787 1906 3111.126 1203.674 89.791 26.89214 1.071574 0.933172 0.09973212 -0.038754
14 3737.76 2999.264 801 1914 2936.759 1085.264 46.3128 22.74929 1.121879 0.8913288 0.1659175 0.029436
15 3332.55 2786.532 810 1910 2522.553 876.532 41.0633 21.90249 1.193125 0.8381042 0.2547455 0.117337
16 3738.37 2884.528 819.5 1907.5 2918.871 977.028 89.4253 29.33896 1.238572 0.8073517 0.3086779 0.178254
17 3334.93 2774.052 814 1905 2520.928 869.052 66.1222 25.21782 1.20262 0.8314875 0.2661806 0.133559
18 2315.707 2390.315 781 1883 1534.707 507.315 40.4415 14.96877 1.254183 0.7973025 0.326748 -0.016545
19 2337.323 2399.521 791 1886.5 1546.323 513.021 43.5795 17.00204 1.249622 0.8002126 0.321492 0.131273
20 2362.364 2397.409 793 1883.5 1569.364 513.909 48.4501 15.18877 1.266049 0.7898297 0.3403337 0.152636

Total number of rows: 53856

Table truncated, full table size 5543 Kbytes.




Supplementary data files not provided
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