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Sample GSM123905 Query DataSets for GSM123905
Status Public on Dec 06, 2006
Title S37
Sample type genomic
 
Channel 1
Source name S37-NA17766
Organism Homo sapiens
Characteristics B-lymphocyte cell line DNA
Biomaterial provider Coriell Cell Repositories
http://locus.umdnj.edu/nigms/nigms_cgi/display.cgi?NA17766
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 4326.68 1865.305 217 348 4109.68 1517.305 395.886 123.1774 1.100491 0.9086444 0.1381477 -0.004644
2 7095.93 2978.859 209 351 6886.93 2627.859 403.084 207.6331 1.064816 0.939087 0.09060477 0.110073
3 6311.71 2693.03 182 344 6129.71 2349.03 315.8012 154.5837 1.060235 0.9431447 0.08438443 0.094938
4 5824.19 2449.627 180 339 5644.19 2110.627 498.98 164.1395 1.086528 0.9203218 0.1197252 0.124342
5 5023.9 2499.581 179 344.5 4844.9 2155.081 417.428 161.6126 0.9134229 1.094734 -0.1306452 -0.128093
6 182.3626 341.516 179.5 341.5 2.86264 0.01647949 0.2323831 -0.1282085 70.5788 0.01416793 6.14116 7.051955
7 8392.8 3747.72 183 343 8209.8 3404.72 671.597 249.6697 0.9797207 1.020653 -0.02955749 0.014771
8 185.7143 344.352 188 346.5 -2.285721 -2.148346 -0.1188524 -0.09294068 0 0 0 0
9 7789.26 3661.11 187.5 347 7601.76 3314.11 626.399 188.8385 0.931963 1.072956 -0.1016554 -0.044974
10 6088.5 2594.885 188.5 345 5900 2249.885 556.589 147.9322 1.065474 0.9385077 0.09149502 0.10243
11 6361.45 3026.71 185.5 343 6175.95 2683.71 540.105 235.0754 0.9350166 1.069452 -0.096936 -0.071388
12 7808.9 2670.109 194 346 7614.9 2324.109 608.501 177.1406 1.331248 0.7511413 0.4127792 0.453405
13 8195.68 3917.42 197 351.5 7998.68 3565.92 673.122 306.1801 0.9113772 1.097191 -0.1338798 -0.06671
14 7254.46 3020.069 197 350.5 7057.46 2669.569 593.313 228.0032 1.074133 0.9309417 0.1031728 0.155909
15 6040.5 2704.175 197 348.5 5843.5 2355.675 557.519 188.1187 1.007881 0.9921364 0.0113251 0.056274
16 6473.56 2803.914 199 348 6274.56 2455.914 529.551 138.4307 1.038057 0.9632948 0.05388616 0.107959
17 6659.73 3094.143 199 349 6460.73 2745.143 357.719 161.5344 0.9562424 1.045713 -0.06455161 0.006143
18 5664.14 2339.681 191 349 5473.14 1990.681 235.2875 148.7305 1.117084 0.8951476 0.1597379 0.004977
19 6143.06 2510.865 185 344.5 5958.06 2166.365 321.554 154.9585 1.117441 0.8948617 0.1601989 0.062948
20 5885.88 2332.937 180 344 5705.88 1988.937 427.547 158.9734 1.16561 0.8578818 0.2210847 0.13038

Total number of rows: 53856

Table truncated, full table size 5451 Kbytes.




Supplementary data files not provided
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