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Sample GSM185462 Query DataSets for GSM185462
Status Public on May 08, 2007
Title Unknown primary site, Melanoma, NOS (13108231)
Sample type genomic
 
Channel 1
Source name TB3074DF1T10
Organism Homo sapiens
Characteristics Tissue
TB3074DF1T10
Growth protocol Unknown primary site; Melanoma, NOS
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from frozen tumors or cultured cells by overnight digestion, phenol-chloroform extraction and ethanol precipitation.
Label Cy5
Label protocol One µg of tumor and reference DNA were labeled with Cy3 or Cy5, respectively (Amersham, Piscataway, NJ) using the BioPrime random-primed labeling kit (Invitrogen, Carlsbad, CA). Labeled tumor and reference DNA were combined and precipitated with human Cot-1 DNA to reduce non-specific binding.
 
Channel 2
Source name pooled reference
Organism Homo sapiens
Characteristics pooled reference
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from frozen tumors or cultured cells by overnight digestion, phenol-chloroform extraction and ethanol precipitation.
Label Cy3
Label protocol One µg of tumor and reference DNA were labeled with Cy3 or Cy5, respectively (Amersham, Piscataway, NJ) using the BioPrime random-primed labeling kit (Invitrogen, Carlsbad, CA). Labeled tumor and reference DNA were combined and precipitated with human Cot-1 DNA to reduce non-specific binding.
 
 
Hybridization protocol DNA was resuspended and hybridized to the array for 72h at 37oC on a rotating platform. Additional details are found in: Greshock, J, Naylor, TL, Margolin, A, et al. 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. Genome Res 2004; 14: 179-87
Scan protocol Images were scanned with an Axon 4500 microarray scanner (Axon, Union City, CA) and analyzed with GenePix 3.0 software (Axon).
Description Unknown primary site; Melanoma, NOS; University of Pennsylvania; 1/14/2005
Data processing All spots were subjected to a pin-tip normalization.
 
Submission date Apr 27, 2007
Last update date May 07, 2007
Contact name Joel Greshock
Organization name GlaxoSmithKline
Department Translational Medicine, Oncology
Street address 2301 Renaissance Blvd.
City King of Prussia
State/province PA
ZIP/Postal code 19406
Country USA
 
Platform ID GPL4894
Series (1)
GSE7692 Cancer cell lines as genetic models of their parent histology: analyses based on array comparative genomic hybridization

Data table header descriptions
ID_REF
SLIDE Slide/Exeriment Identifier
Dia Spot Diameter in Pixels
F635_Median Median foreground measurement of Cy5 channel
F635_Mean Mean foreground measurement of Cy5 channel
F635_SD Standard Deviation of foreground measurement of Cy5 channel
B635_Median Median background of Cy5 channel
B635_Mean Mean background of Cy5 channel
B635_SD Standard deviation of background of Cy5 channel
PCT_GT_B635_1SD Percent of pixels > 1 standard deviation above background for Cy5 channel
PCT_GT_B635_2SD Percent of pixels > 2 standard deviation above background for Cy5 channel
F635_PCT_Sat Percent of pixels that are saturated for Cy5 channel
F532_Median Median foreground measurement of Cy3 channel
F532_Mean Mean foreground measurement of Cy3 channel
F532_SD Standard Deviation of foreground measurement of Cy3 channel
B532_Median Median background of Cy3 channel
B532_Mean Mean background of Cy3 channel
B532_SD Standard deviation of background of Cy3 channel
PCT_GT_B532_1SD Percent of pixels > 1 standard deviation above background for Cy5 channel
PCT_GT_B532_2SD Percent of pixels > 2 standard deviation above background for Cy5 channel
F532_PCT_Sat Percent of pixels that are saturated for Cy3 channel
Ratio_of_Medians_532_635 Ratio of median pixel values (Cy3/Cy5)
Ratio_of_Means_532_635 Ratio of mean pixel values (Cy3/Cy5)
Median_of_Ratios_532_635 Median of all individual pixel ratios (Cy3/Cy5)
Mean_of_Ratios_532_635 Mean of all individual pixel ratios (Cy3/Cy5)
Ratios_SD_532_635 Standard deviation of all individual pixel ratios (Cy3/Cy5)
Rgn_Ratio_532_635 Red to green ratio
Rgn_R2_532_635 Red to green correlation
F_Pixels The number of pixels analyzed as foreground (both Cy3 and Cy5 uses same exact pixels)
B_Pixels The number of pixels analyzed as background (same for Cy3 and Cy5)
Sum_of_Medians Sum of Pixel intensity medians
Sum_of_Means Sum of Pixel intensity means
Log_Ratio_532_635 Log base 2 of the Cy3/Cy5 ratio
F635_Median_B635 Median Foreground intensity minus Background intensity, Cy5 channel
F532_Median_B532 Median Foreground intensity minus Background intensity, Cy3 channel
F635_Mean_B635 Mean Foreground intensity minus Background intensity, Cy5 channel
F532_Mean_B532 Mean Foreground intensity minus Background intensity, Cy3 channel
Ratio_Median Median Cy3/Cy5 ratio (using the Background corrected ratio of medians) for that specific print tip
Cy3_corrected Adjusted background corrected intensity (by print tip)= F532_Median_B532 / Ratio_Median_Tip
VALUE log(GREENsignal/REDsignal) per feature (processed signals used).
A mean log intensity
Sig_var_mean_Cy3 Signal variation from mean intsity for Cy3 channel
Sig_var_mean_Cy5 Signal variation from mean intsity for Cy5 channel
Mean_med_corr_Cy3 Mean-Median correlation for Cy3 channel
Mean_med_corr_Cy5 Mean-Median correlation for Cy5 channel

Data table
ID_REF SLIDE Dia F635_Median F635_Mean F635_SD B635_Median B635_Mean B635_SD PCT_GT_B635_1SD PCT_GT_B635_2SD F635_PCT_Sat F532_Median F532_Mean F532_SD B532_Median B532_Mean B532_SD PCT_GT_B532_1SD PCT_GT_B532_2SD F532_PCT_Sat Ratio_of_Medians_532_635 Ratio_of_Means_532_635 Median_of_Ratios_532_635 Mean_of_Ratios_532_635 Ratios_SD_532_635 Rgn_Ratio_532_635 Rgn_R2_532_635 F_Pixels B_Pixels Sum_of_Medians Sum_of_Means Log_Ratio_532_635 F635_Median_B635 F532_Median_B532 F635_Mean_B635 F532_Mean_B532 Ratio_Median Cy3_corrected VALUE A Sig_var_mean_Cy3 Sig_var_mean_Cy5 Mean_med_corr_Cy3 Mean_med_corr_Cy5
RP11-458D3 13108231 140 18488.5 18487 3399.5 958 1220.5 1746 100 100 0 19855 19224.5 4065 737.5 1082.5 2223 100 99 0 1.0905 1.0545 1.066 1.0425 1.232 1.0755 0.947 156 611 36648 36016 0.125 17530.5 19117.5 17529 18487 0.9515 20091.9600630583 1.14612376830084 14.1600756508616 0.788418479516015 0.815725614466337 0.966999322116158 0.988512143977318
RP11-69E9 13108231 145 14544.5 15212 4086.5 938 1156 1500.5 100 99.5 0 20087.5 20912 6010 802.5 1018.5 1527 99.5 99.5 0 1.418 1.4105 1.4055 1.4045 1.166 1.4365 0.9645 156 725 32891.5 34383.5 0.5035 13606.5 19285 14274 20109.5 0.9465 20375.0660327522 1.49790269559274 13.9811421683516 0.71208829909585 0.731437665786088 0.959199545393379 0.954146111273068
RP11-67E18 13108231 125 3341.5 3380.5 1026 1060.5 1414.5 1945 61 22.5 0 2608 2633 642.5 865 1197.5 1957.5 44.5 4.5 0 0.764 0.7625 0.7595 0.799 1.6475 0.698 0.686 120 589.5 4024 4088 -0.388 2281 1743 2320 1768 0.912 1911.18421052631 0.837873259189303 10.9613941070409 0.756437552679282 0.696423680417793 0.986108261980616 0.97966413765524
RP11-291C17 13108231 150 9335.5 9538 2746.5 916 1126 949.5 99 99 0 9647 10231 3245.5 794.5 1021.5 993 99.5 99 0 1.0525 1.096 1.072 1.0955 1.2155 1.1205 0.945 156 917.5 17272 18058.5 0.073 8419.5 8852.5 8622 9436.5 0.938 9437.63326226013 1.12180275739461 13.0748539324828 0.682542820911926 0.711417591467088 0.938020916415669 0.976743267402637
RP11-506N24 13108231 130 11001.5 10886 2274 963.5 1111.5 788 100 99.5 0 9561 9370 1983 771 888.5 644.5 100 100 0 0.8745 0.8655 0.8805 0.867 1.234 0.8795 0.938 120 616.5 18828 18521.5 -0.1935 10038 8790 9922.5 8599 0.9395 9356.04044704629 0.931039541126869 13.1936489996478 0.788599659654821 0.790692010314533 0.97664898723471 0.976672169360723
RP11-262N9 13108231 140 14963 14530.5 3666 1061.5 1137 604.5 99.5 99.5 0 15131 14429 3996 805.5 854.5 384.5 99 98.5 0 1.031 1.011 1.023 0.9715 1.4165 1.0215 0.9545 156 668 28227 27092.5 0.0435 13901.5 14325.5 13469 13623.5 0.912 15707.7850877193 1.1301701939814 13.7838537464873 0.723495988160156 0.747962476139461 0.950725671485651 0.969371875261647
RP11-498J1 13108231 140 9510 9967.5 2612.5 928 1391.5 2508 99.5 94.5 0 9237 10033.5 3061.5 782 1218 2416 98 96.5 0 0.9845 1.025 1.021 1.009 1.263 1.046 0.94 156 663.5 17037 18291 -0.022 8582 8455 9039.5 9251.5 0.9795 8631.955079122 1.00559658972986 13.0533377006062 0.694371764639963 0.737079620741247 0.913013187958613 0.949633216693568
RP11-335F1 13108231 150 6769.5 7146 2158 929.5 1074 1013 100 98 0 7778.5 8349.5 2462.5 787 919 1140 100 98 0 1.1985 1.2175 1.2065 1.231 1.248 1.243 0.926 156 689 12831.5 13779 0.261 5840 6991.5 6216.5 7562.5 0.912 7666.11842105263 1.31415174143384 12.6400158652775 0.705640875759161 0.698434874886049 0.924598000629472 0.939367289977305
RP11-260B11 13108231 145 7854 8082 2627 955 1039 547 100 100 0 7477.5 7644.5 2630.5 735.5 797.5 380.5 100 100 0 0.9815 0.9705 0.974 0.968 1.3025 0.996 0.922 156 682.5 13641 14036 -0.0285 6899 6742 7127 6909 0.9015 7478.64669994454 1.08859817079625 12.7312768204323 0.654714576220616 0.672791079554365 0.975353617417664 0.964046376681508
RP11-367E10 13108231 150 8122.5 8237 1926.5 946 1031 623 100 100 0 9404.5 9673.5 2064.5 732 817.5 534 100 100 0 1.2075 1.225 1.225 1.238 1.2445 1.248 0.9275 156 698 15849 16232.5 0.2715 7176.5 8672.5 7291 8941.5 0.912 9509.32017543861 1.32381378577658 12.9433742109805 0.786453474868213 0.766687412878503 0.970524382908257 0.984727503570239
CTD-2341I10 13108231 145 15215.5 15196.5 3474 898 1059 1222 100 99.5 0 11325.5 11195 2614.5 775 890 990 100 99 0 0.741 0.7325 0.73 0.7285 1.175 0.736 0.966 156 700 24868 24718.5 -0.434 14317.5 10550.5 14298.5 10420 0.9465 11146.8568409931 0.782834754123894 13.5788612151688 0.766569925920288 0.770726162442849 0.987271182399291 0.998533659731134
RP11-490K2 13108231 140 13203 13204 3559 963 1186.5 1394.5 100 99.5 0 13486.5 13586.5 4089 740.5 1035 1777.5 100 97.5 0 1.0395 1.049 1.0665 1.039 1.2285 1.073 0.936 156 675 24986 25087 0.0555 12240 12746 12241 12846 0.936 13617.5213675214 1.1103754282448 13.6023844044437 0.696486683677884 0.72854490095723 0.977355024821043 0.997694819892067
RP11-491P10 13108231 135 18230.5 17622.5 4047 998.5 1196 1197 99 99 0 17398.5 16654.5 3490 771 966.5 1222.5 99.5 99 0 0.9655 0.9555 0.9475 0.974 1.2355 0.9485 0.966 138 636 33859.5 32507.5 -0.0505 17232 16627.5 16624 15883.5 0.912 18231.9078947369 1.05858879590398 14.0458304216804 0.790138781774633 0.770587984712833 0.954837376998429 0.964630204375208
RP11-43H17 13108231 145 8510 8682.5 2226.5 918 1056.5 799.5 100 99 0 9595.5 9914 2416 804.5 942.5 823 99.5 99.5 0 1.1615 1.176 1.1805 1.1815 1.283 1.1725 0.933 156 676.5 16383 16874 0.215 7592 8791 7764.5 9109.5 0.9465 9287.9027997887 1.22715622843447 12.9922752002597 0.75433092574882 0.741968816798021 0.965797963417156 0.977788089207087
RP11-492D3 13108231 155 9715.5 9911.5 3072.5 928.5 1014 494.5 99.5 99.5 0 10332.5 10512 3324.5 763.5 809.5 364 100 99 0 1.088 1.0845 1.079 1.08 1.262 1.0965 0.9475 182 704.5 18356 18731.5 0.122 8787 9569 8983 9748.5 0.912 10492.3245614035 1.1933160704233 13.1605789617893 0.686717307853667 0.691949396164713 0.980878387209351 0.976923898385482
RP11-97J12 13108231 150 15752.5 16149.5 4950 1025.5 1139.5 833 99 99 0 13594.5 14291 4225 821.5 942.5 750 100 100 0 0.8675 0.8905 0.871 0.903 1.2725 0.886 0.957 156 700 27500 28593.5 -0.206 14727 12773 15124 13469.5 0.912 14005.4824561404 0.950951789177999 13.7433012546605 0.704687766981855 0.693810670426336 0.948222693524992 0.973836443371285
RP11-541N19 13108231 150 12905.5 13353 3496 1001 1048.5 503.5 100 100 0 9963.5 10219 2341 822 872.5 391.5 100 100 0 0.769 0.762 0.7695 0.7685 1.2 0.7525 0.9545 156 699 21046 21749 -0.3795 11904.5 9141.5 12352 9397 0.912 10023.5745614035 0.843271350198213 13.34480480475 0.770394884521638 0.736943744794396 0.972276970093434 0.962915681772985
RP11-25L9 13108231 150 13612.5 14719 4678 960 1309 2105 100 100 0 13069 14052.5 4488.5 752 1031 1525.5 100 99.5 0 0.9735 0.967 0.9625 0.9655 1.171 0.981 0.958 156 685.5 24969.5 27059.5 -0.0385 12652.5 12317 13759 13300.5 0.912 13505.4824561403 1.06742179233719 13.6077442009861 0.680587330927783 0.68217144413821 0.926121482691691 0.919718558795231
RP11-347O8 13108231 140 14618.5 14608.5 4656 973.5 1070.5 638 100 99.5 0 10085.5 10105 3347.5 754 834 497.5 100 99.5 0 0.6835 0.686 0.685 0.681 1.221 0.694 0.9545 156 668 22976.5 22986 -0.5495 13645 9331.5 13635 9351 0.9015 10351.081530782 0.758204983731095 13.4610793523374 0.667533964382334 0.680615461330692 0.995231757274847 0.974614706475905
RP11-518H12 13108231 150 8707 8667 2549 972.5 1344.5 1863.5 97.5 94 0 10447 10561 3166.5 721.5 1127 2038 97.5 96 0 1.2605 1.278 1.2625 1.2805 1.2875 1.3235 0.8805 156 709.5 17460 17534 0.333 7734.5 9725.5 7694.5 9839.5 0.9515 10221.2296374146 1.32429435323005 13.0800785236346 0.696204947624012 0.702547622935881 0.972549141677428 0.98367522278876

Total number of rows: 3857

Table truncated, full table size 1304 Kbytes.




Supplementary file Size Download File type/resource
GSM185462.gpr.gz 856.8 Kb (ftp)(http) GPR

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