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Sample GSM185449 Query DataSets for GSM185449
Status Public on May 08, 2007
Title Unknown primary site, Malignant melanoma, NOS (12933428)
Sample type genomic
 
Channel 1
Source name TB2666DF1T10
Organism Homo sapiens
Characteristics Tissue
TB2666DF1T10
Growth protocol Unknown primary site; Malignant 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; Malignant melanoma, NOS; University of Pennsylvania; 8/17/2004
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 12933428 125 1254 1200 491 85.5 117.5 149.5 92.5 90.5 0 1199 1164.5 576 79 125 212.5 85.5 83 0 0.9585 0.974 1.0325 0.835 2.133 1.063 0.791 120 640.5 2288.5 2200 -0.062 1168.5 1120 1114.5 1085.5 0.9965 1123.93376818866 0.961566583221111 10.1574299128185 0.502682227379562 0.588502585205995 0.969762581454596 0.954024736415247
RP11-69E9 12933428 130 1444.5 1545 590 86.5 113.5 163 97 95.5 0 1457 1581.5 732.5 80.5 116.5 217 91.5 89.5 0 1.0115 1.028 1.0595 0.9005 2.054 1.0785 0.815 120 753 2734.5 2959.5 0.016 1358 1376.5 1458.5 1501 1.0835 1270.41993539456 0.933840746655909 10.4132559987791 0.533316720317879 0.615871084593808 0.915709169996234 0.930935470492313
RP11-67E18 12933428 100 134 132 44 89 100.5 84 15 0.5 0 147 142.5 43.5 80 89 50.5 52 16.5 0 1.518 1.3485 1.456 1.1775 3.5395 0.8065 0.1645 66 486 112 105.5 0.6015 45 67 43 62.5 1.1395 58.7977182974989 1.33193197585475 5.40537347004515 0.708333333333333 0.661463414634146 0.943302752293578 0.82014157014157
RP11-291C17 12933428 125 550.5 679.5 415.5 85 94.5 50.5 95 92 0 478.5 683 492.5 79 86 56.5 88.5 85.5 0 0.8585 1.019 1.046 0.873 2.728 1.1895 0.741 120 706 865 1198.5 -0.22 465.5 399.5 594.5 604 1.096 364.507299270073 0.783308157619536 8.75142113544639 0.279581640201997 0.389186681673395 0.661266263590123 0.784168124900575
RP11-506N24 12933428 130 600 591 171.5 83 113 183 94 82.5 0 815 784.5 284 74 106 197 91.5 89 0 1.4315 1.397 1.421 1.268 1.945 1.5185 0.858 120 666 1258 1218.5 0.5175 517 741 508 710.5 1.053 703.703703703703 1.35972114916157 9.26874410898006 0.639593933511759 0.710564860766474 0.959418972876222 0.983372716053099
RP11-262N9 12933428 120 1262.5 1158 464.5 103.5 124 139 92.5 90 0 1296.5 1169 526 89.5 111.5 119.5 90 85.5 0 1.0395 1.0235 1.0045 0.9505 1.588 1.044 0.928 120 612.5 2366 2134 0.055 1159 1207 1054.5 1079.5 1.1395 1059.23650724002 0.91232150781652 10.2047311687859 0.547836216616165 0.596598000512996 0.8961696279952 0.909388259529334
RP11-498J1 12933428 105 551 550 182 83.5 100 95.5 97 92.5 0 582.5 566 239 80 101.5 120.5 89 82.5 0 1.083 1.0405 1.056 0.9235 2.005 1.174 0.7235 80 567 970 952.5 0.111 467.5 502.5 466.5 486 1.0735 468.095016301816 1.0087755063939 8.91709188333336 0.576899363097194 0.66888172576246 0.962351478308926 0.921669243708902
RP11-335F1 12933428 135 383.5 384.5 200 104 127 121 86.5 60.5 0 612 562.5 226.5 90.5 131 181.5 85 73 0 1.866 1.6825 1.766 1.5695 2.398 1.7105 0.652 138 701 801 752.5 0.9 279.5 521.5 280.5 472 1.1395 457.656867046951 1.63762523393981 8.57353895395811 0.596937321937322 0.479609713203463 0.905739551026436 0.937547938638543
RP11-260B11 12933428 135 406.5 416.5 163.5 80 85.5 37 95.5 94.5 0 437.5 420 179 73.5 79.5 38.5 92 89 0 1.1145 1.0295 1.054 0.9145 2.255 1.0805 0.7885 138 679 690.5 683 0.1565 326.5 364 336.5 346.5 1.0395 350.16835016835 1.07236166904053 8.42915120275354 0.573284174702212 0.606914703474361 0.951809230397487 0.970371548205862
RP11-367E10 12933428 135 296.5 326 149 100.5 131.5 123.5 71 47.5 0 448.5 468.5 222 85.5 136.5 205.5 76 49 0 1.8515 1.696 1.8965 1.6815 2.319 1.812 0.667 138 676.5 559 608.5 0.889 196 363 225.5 383 1.1395 318.560772268539 1.62471713408156 8.05355105795388 0.524935733823678 0.542482614546378 0.946684219187099 0.867727523224689
CTD-2341I10 12933428 125 568.5 591 295 83.5 92 53 94 92 0 552.5 600.5 326 80.5 92.5 73.5 87.5 85 0 0.9735 1.022 1.0915 0.9415 2.106 1.0895 0.775 120 650.5 957 1027.5 -0.0405 485 472 507.5 520 1.0835 435.625288417166 0.898703967050595 8.9014889985611 0.455507209996374 0.499951241338167 0.91224337439343 0.938394049208468
RP11-490K2 12933428 125 566 548.5 225 80.5 111.5 140 93.5 75 0 585.5 555 265.5 74 130.5 238.5 79.5 52.5 0 1.0515 1.027 1.074 0.925 2.1895 1.086 0.799 120 676 997 949 0.0715 485.5 511.5 468 481 1.056 484.375 0.995814596736635 8.95737267498123 0.519654498044329 0.589493471439208 0.941373453699567 0.963556628632774
RP11-491P10 12933428 105 495.5 495.5 179.5 90.5 98.5 47 94 91 0 555.5 541.5 236 78.5 86.5 39.5 90 86.5 0 1.158 1.1015 1.0775 0.9815 1.9415 1.167 0.755 80 520 882 868 0.211 405 477 405 463 1.1395 418.604651162791 1.01643146996489 8.5562265761573 0.581943134837165 0.643645906015836 0.943923182441701 0.986787108503161
RP11-43H17 12933428 125 547 542 188.5 86 98 73 95.5 91.5 0 842.5 814.5 335.5 81 101.5 117 91.5 90.5 0 1.666 1.617 1.6755 1.477 1.8625 1.7865 0.7895 120 651 1222.5 1189.5 0.734 461 761.5 456 733.5 1.0835 702.814951545916 1.537564464624 9.19929590764921 0.586993238144112 0.64756980138986 0.948040011459129 0.945330988167573
RP11-492D3 12933428 140 435 455 215 98 115.5 98 84 73.5 0 481.5 498 276.5 84 112.5 146 78.5 63 0 1.175 1.1565 1.1565 1.008 2.323 1.252 0.7865 156 691 734.5 771 0.232 337 397.5 357 414 1.1395 348.837209302326 1.03105342491693 8.4989959348601 0.437525280382424 0.521066082511865 0.955998954689347 0.941133028397179
RP11-97J12 12933428 130 766 768 192 88 107.5 91 98.5 94 0 824.5 792 257 83 101.5 99 95 93.5 0 1.1345 1.0965 1.1115 1.034 2.0195 1.114 0.7635 120 667.5 1419.5 1389 0.1805 678 741.5 680 709 1.1395 650.724001755157 0.995593934874349 8.93250919604703 0.683155211295225 0.735473205675713 0.964640863554028 0.995091644688957
RP11-541N19 12933428 130 447.5 460 155.5 101.5 154 215 85 28 0 504.5 490 179.5 92 155.5 265 81.5 21 0 1.1935 1.1095 1.164 1.0425 1.9185 1.136 0.747 120 689 758.5 756.5 0.2545 346 412.5 358.5 398 1.1395 362.000877577885 1.04737319138275 8.56100040272983 0.632878151260505 0.66138151425762 0.964720194647202 0.964881276761385
RP11-25L9 12933428 140 992.5 972.5 329 92 107.5 83 97 94 0 1141 1029 410 80 96.5 87 92 90 0 1.181 1.078 1.071 0.955 1.831 1.1225 0.881 138 618.5 1961.5 1829.5 0.238 900.5 1061 880.5 949 1.1395 931.110136024573 1.03639289329838 9.93209013842452 0.60117200672147 0.661786941580756 0.894421066751235 0.958973111172446
RP11-347O8 12933428 135 667.5 672.5 352 82 91.5 60.5 95.5 92 0 613 606.5 344 74 87.5 72.5 90 78.5 0 0.919 0.9 0.9355 0.815 2.361 0.947 0.799 138 666 1124.5 1123 -0.1215 585.5 539 590.5 532.5 1.0395 518.518518518518 0.884414492538746 9.11578445291822 0.430479912244618 0.476751523015193 0.947035480073987 0.929314507878043
RP11-518H12 12933428 125 463.5 470 177.5 84 106 99 96 84.5 0 651 626 244 77 113.5 158.5 91.5 83 0 1.512 1.4235 1.4755 1.258 2.209 1.5495 0.7565 120 664 953.5 935 0.5955 379.5 574 386 549 0.9965 576.016056196689 1.51722696103027 8.8656400148902 0.610325426567143 0.622906393903582 0.957384428223845 0.968075824873097

Total number of rows: 3842

Table truncated, full table size 1216 Kbytes.




Supplementary file Size Download File type/resource
GSM185449.gpr.gz 784.5 Kb (ftp)(http) GPR

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