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Sample GSM123906 Query DataSets for GSM123906
Status Public on Dec 06, 2006
Title S38
Sample type genomic
 
Channel 1
Source name S38-NA17076
Organism Homo sapiens
Characteristics B-lymphocyte cell line DNA
Biomaterial provider Coriell Cell Repositories
http://locus.umdnj.edu/nigms/nigms_cgi/display.cgi?NA17076
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 2572.25 1265.119 187 338 2385.25 927.119 197.7777 77.9339 1.184471 0.844229 0.2442434 0.025088
2 3850.9 1768.796 189 343 3661.9 1425.796 331.559 114.4837 1.182431 0.8456859 0.2417559 0.083846
3 3089.455 1382.25 190 339 2899.455 1043.25 275.841 76.9283 1.279541 0.7815032 0.355626 0.18269
4 2918.253 1341.414 190 340 2728.253 1001.414 233.2396 77.0352 1.254288 0.7972373 0.3268685 0.153282
5 2663.589 1392.711 194 341 2469.589 1051.711 157.7794 86.9231 1.081071 0.9249761 0.1124618 -0.063558
6 3247.2 1456.506 215 345 3032.198 1111.506 117.7008 70.608 1.255948 0.7961833 0.3287771 0.158138
7 4361.84 2133.205 230 347 4131.84 1786.205 141.3403 115.6209 1.064973 0.9389579 0.09081735 -0.054646
8 3938.57 1906.909 277 358 3661.57 1548.909 163.4597 96.9465 1.088348 0.9187917 0.1221399 -0.031366
9 4060.24 2059.177 267 352 3793.24 1707.177 198.0258 118.0811 1.022957 0.9775237 0.03274597 -0.109767
10 3320.1 1596.585 249 351 3071.098 1245.585 104.8591 100.9291 1.135132 0.8809242 0.1828599 0.014185
11 2737.739 1489.228 193.5 344.5 2544.239 1144.728 125.2272 79.2805 1.02325 0.9772444 0.03315844 -0.134878
12 3904.2 1385.782 191.5 339 3712.7 1046.782 388.264 76.8395 1.632899 0.6123863 0.7074357 0.555469
13 3559.21 1835.769 194 339 3365.21 1496.769 298.3596 122.5332 1.035102 0.9660543 0.04977347 -0.090978
14 3861.06 1780.976 193.5 339 3667.56 1441.976 280.9517 116.1509 1.170968 0.8539644 0.2277019 0.093803
15 2621.209 1272.174 189 340 2432.209 932.174 181.4173 58.3922 1.20124 0.8324438 0.2645248 0.112538
16 3050.279 1441.535 184.5 336.5 2865.779 1105.035 244.2438 61.3052 1.193969 0.8375138 0.2557648 0.120001
17 3199.95 1488.989 183 338 3016.954 1150.989 249.5729 78.3204 1.206768 0.8286306 0.2711487 0.148784
18 2551.805 1178.586 179 337 2372.805 841.586 210.0759 65.0636 1.298044 0.7703627 0.3763398 -0.04045
19 2677.138 1198.701 179 339 2498.138 859.701 50.7414 22.92743 1.337812 0.7474632 0.4198753 0.155294
20 2464.059 1112.788 179.5 336.5 2284.559 776.288 204.6425 51.9928 1.354895 0.738039 0.4381807 0.1725

Total number of rows: 53856

Table truncated, full table size 5509 Kbytes.




Supplementary data files not provided
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