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Sample GSM123907 Query DataSets for GSM123907
Status Public on Dec 06, 2006
Title S39
Sample type genomic
 
Channel 1
Source name S39-NA15729
Organism Homo sapiens
Characteristics B-lymphocyte cell line DNA
Biomaterial provider Coriell Cell Repositories
http://locus.umdnj.edu/nigms/nigms_cgi/display.cgi?NA15729
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 1909.884 862.605 157 331 1752.884 531.605 42.8487 25.90175 1.210142 0.8263221 0.275176 -0.021099
2 2768.326 1102.742 161 333 2607.326 769.742 257.6134 48.7934 1.243147 0.8043837 0.3139963 0.061843
3 2350.674 950.584 159 332 2191.674 618.584 181.6253 46.1646 1.300316 0.7690181 0.3788627 0.117519
4 2291.282 955.329 160 336 2131.282 619.329 145.6255 46.225 1.262965 0.7917614 0.3368145 0.078212
5 1975.143 937.06 171 335.5 1804.143 601.56 158.3816 53.328 1.100688 0.9084925 0.1384056 -0.115278
6 2450.192 979.026 169 336 2281.192 643.026 195.8574 59.2059 1.301984 0.7680332 0.3807114 0.143732
7 2899.129 1222.024 169 335.5 2730.129 886.524 275.3139 67.0266 1.130225 0.8847502 0.1766099 -0.037138
8 2677.531 1124.062 164 334 2513.531 790.062 263.3297 68.9263 1.167603 0.8564273 0.2235494 0.008887
9 2777.286 1342.516 159 331.5 2618.286 1011.016 296.3252 90.9619 0.9504532 1.052095 -0.07331259 -0.262053
10 2419.035 1035.581 160 332 2259.035 703.581 133.7329 42.8986 1.178367 0.848604 0.2367887 0.023575
11 2363.241 1187.874 156.5 331 2206.741 856.874 198.3981 64.9436 0.9451629 1.057984 -0.08136518 -0.276075
12 2752.42 1033.523 161 331 2591.42 702.523 219.4348 51.5743 1.353784 0.7386456 0.4369978 0.254401
13 2970.682 1480.216 159.5 332.5 2811.182 1147.716 241.3937 96.1741 0.8989313 1.112395 -0.1537174 -0.299963
14 2556.098 1225.561 158 332 2398.098 893.561 211.5856 73.1142 0.9849509 1.015245 -0.02187628 -0.183837
15 2202.707 1091.89 155 332 2047.707 759.89 177.6946 65.3845 0.9889832 1.011106 -0.0159821 -0.182318
16 2260.165 1069.094 151 334 2109.165 735.094 177.5303 71.5811 1.053027 0.9496117 0.07454234 -0.087547
17 2298.295 1222.557 158 328 2140.295 894.557 186.0368 79.568 0.8780874 1.138801 -0.1875636 -0.33775
18 2393.472 1013.461 158 331 2235.472 682.461 243.4549 39.5353 1.202163 0.8318061 0.265633 -0.011222
19 2408.057 1049.807 159 329 2249.057 720.807 266.3923 39.6332 1.145127 0.8732368 0.1955071 -0.097509
20 1928.558 813.628 158 332 1770.558 481.628 189.8282 42.0547 1.349182 0.7411653 0.4320847 0.116289

Total number of rows: 53856

Table truncated, full table size 5497 Kbytes.




Supplementary data files not provided
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