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Sample GSM185174 Query DataSets for GSM185174
Status Public on May 08, 2007
Title Skin of forearm, Superficial spreading melanoma (C44._) (12430304)
Sample type genomic
 
Channel 1
Source name TB0258DF1X10
Organism Homo sapiens
Characteristics Cell Line WM 1361A
TB0258DF1X10
Growth protocol Skin of forearm; Superficial spreading melanoma (C44._)
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.
 
Channel 2
Source name female
Organism Homo sapiens
Characteristics female
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.
 
 
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 Skin of forearm; Superficial spreading melanoma (C44._); University of Pennsylvania; 11/29/2002
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 12430304 210 9105.5 9926.5 5323 296 458 850 99.5 98 0 4769 5116.5 2338 784 845.5 441 98.5 96 0 0.4515 0.4485 0.4505 0.4425 1.316 0.4375 0.937 316 1005.5 12794.5 13963 -1.1475 8809.5 3985 9630.5 4332.5 0.435 9160.91954022991 1.03838498093666 12.5272974379794 0.548997722699791 0.466645493094781 0.923008325804151 0.915927448041107
RP11-67E18 12430304 235 17014.5 18589 8319 323 431.5 629.5 100 99.5 0 6895 7394.5 3499.5 933.5 962.5 301 100 99.5 0 0.3585 0.3555 0.35 0.3555 1.2205 0.358 0.9025 426 1365 22653 24727 -1.4815 16691.5 5961.5 18266 6461 0.3905 15266.3252240717 0.917512787541999 13.2826104112549 0.530147811264514 0.551417318254154 0.924185767547103 0.917360990624357
RP11-291C17 12430304 215 27688 28090.5 7614.5 281.5 355 344 100 100 0 9994 10214 2728.5 729 750.5 239.5 100 100 0 0.341 0.344 0.342 0.3465 1.16 0.3425 0.962 354 1532 36671.5 37294 -1.553 27406.5 9265 27809 9485 0.439 21104.7835990888 0.776215502835812 13.927322635538 0.715968340202196 0.709706867184986 0.971593255714911 0.974766157773342
RP11-506N24 12430304 215 18867 19789 7377.5 259.5 314 261.5 100 100 0 7383.5 7769.5 2921 767 790 217.5 100 100 0 0.3555 0.3585 0.3525 0.354 1.1905 0.3605 0.9535 354 987 25224 26532 -1.4925 18607.5 6616.5 19529.5 7002.5 0.439 15071.7539863326 0.809089504314948 13.4330298284513 0.631049119861531 0.630474402678209 0.94385751332274 0.951861455150615
RP11-498J1 12430304 205 10667 11078 4715.5 243 301 294 100 100 0 6340.5 6723 2348 725 747.5 215 100 100 0 0.5355 0.5505 0.552 0.5545 1.215 0.534 0.94 316 1536 16039.5 16833 -0.9025 10424 5615.5 10835 5998 0.4335 12953.8638985006 1.23599138603575 12.8878151402921 0.64958807732748 0.576774399241065 0.93513920911998 0.960338400017369
RP11-335F1 12430304 215 9546 11179.5 5845 384 619.5 1415.5 99 97.5 0 3901.5 4489.5 2100.5 958 1031.5 497.5 99.5 97.5 0 0.3235 0.3295 0.3265 0.323 1.2855 0.3305 0.927 354 1136 12105.5 14327 -1.6295 9162 2943.5 10795.5 3531.5 0.404 7285.89108910891 0.800774351063748 12.329727696086 0.532931604276492 0.475674647306074 0.838687867690707 0.85452377473282
RP11-501C13 12430304 220 9234 9976 4508 267 336 295 100 99.5 0 3926 4274 1796 769.5 786 228.5 99.5 99 0 0.352 0.361 0.3565 0.354 1.2505 0.366 0.948 392 1067.5 12123.5 13213.5 -1.506 8967 3156.5 9709 3504.5 0.439 7190.20501138952 0.802038872230933 12.374573950194 0.579373376650927 0.547289207058066 0.90109647708552 0.923011314300013
RP11-367E10 12430304 210 18551.5 19209.5 6726 311.5 383.5 443.5 100 100 0 7269 7451 2888.5 908 929 244 100 100 0 0.349 0.346 0.3375 0.345 1.2005 0.3555 0.905 316 1259.5 24601 25441 -1.5195 18240 6361 18898 6543 0.404 15745.0495049505 0.863933667237429 13.3946586208949 0.6148823960539 0.650631560555945 0.967053781260004 0.965212032950006
RP11-338J16 12430304 215 11133.5 11853 5440 345.5 536 804 97.5 96.5 0 5667 5996.5 2560 851.5 924 414 97.5 96 0 0.4475 0.447 0.445 0.4425 1.314 0.4475 0.9615 354 1565 15603.5 16652.5 -1.1605 10788 4815.5 11507.5 5145 0.433 11121.247113164 1.03428791184187 12.8085415683243 0.562628380605027 0.527125598707048 0.938133838612836 0.936573306409134
RP11-490K2 12430304 210 19806 19719.5 5126.5 272.5 351 567 100 100 0 8427 8269.5 2050.5 720 748 262.5 100 100 0 0.396 0.39 0.3885 0.389 1.159 0.389 0.9685 316 1225 27240.5 26996.5 -1.338 19533.5 7707 19447 7549.5 0.4335 17778.5467128028 0.913492596708678 13.5799636370155 0.752433172307454 0.741244709818325 0.979225762600205 0.983948976693149
RP11-491P10 12430304 230 41768 44780.5 11142.5 453.5 1063.5 1774 99.5 99.5 3 14509.5 16332 5372.5 1013 1185.5 728.5 100 100 0 0.3265 0.345 0.3275 0.341 1.337 0.35 0.92 392 1016 54811 59646 -1.616 41314.5 13496.5 44327 15319 0.3905 34562.099871959 0.83562943268525 14.5253854257551 0.673615157687719 0.751240349326353 0.881594242577183 0.932396508866932
RP11-492D3 12430304 215 14466.5 15359.5 5123.5 295.5 382 457.5 100 100 0 6062.5 6383 1979 799 837 415.5 100 99.5 0 0.371 0.3705 0.368 0.3695 1.1835 0.369 0.949 354 997 19434.5 20648 -1.431 14171 5263.5 15064 5584 0.439 11989.749430524 0.845490875989839 13.0745907821211 0.690629437436327 0.667453288200813 0.942172293260291 0.940779551952184
RP11-541N19 12430304 210 11290.5 13384 7460.5 296.5 354 281 100 100 0 5278 6065 2771 928.5 949.5 245.5 100 100 0 0.398 0.393 0.3945 0.3935 1.2285 0.379 0.947 316 1193 15343.5 18224 -1.33 10994 4349.5 13087.5 5136.5 0.404 10766.0891089109 0.984486843810341 12.7428504261705 0.538702109950212 0.42959749589627 0.847787232575321 0.838184786128381
RP11-25L9 12430304 205 25731.5 25475 8543.5 327 428.5 478 100 100 0 13050 13286 4063.5 896 930 301.5 100 100 0 0.479 0.493 0.4955 0.496 1.147 0.4865 0.9725 316 1147 37558.5 37538 -1.062 25404.5 12154 25148 12390 0.42 28938.0952380953 1.14026380497942 14.0998989366337 0.694758710892836 0.665648904555306 0.981610016563863 0.989749442873562
RP11-518H12 12430304 220 9396 10355.5 4924 258.5 410 634.5 100 99 0 4153.5 4473.5 1832.5 746.5 793 331 100 98.5 0 0.3725 0.3685 0.3645 0.3675 1.233 0.365 0.9395 354 1088 12544.5 13824 -1.4245 9137.5 3407 10097 3727 0.435 7832.18390804597 0.855607505667733 12.4270926748924 0.615096284676423 0.551608074576491 0.929489887583115 0.919212974713976
RP11-35P20 12430304 205 19157.5 21268 7722.5 343 481.5 789 100 100 0 9053.5 9641.5 3099 952 982 295.5 100 100 0 0.432 0.417 0.415 0.418 1.1625 0.4135 0.971 316 1140 26916 29614.5 -1.2145 18814.5 8101.5 20925 8689.5 0.378 21432.5396825397 1.14325625121851 13.5906897644863 0.6780442747047 0.638752462765211 0.932237540084165 0.899642034885415
RP11-366L14 12430304 210 8375.5 9951 6336 251 325 395.5 100 100 0 4465.5 5084 2649 760 789.5 248 100 100 0 0.456 0.4455 0.4515 0.4505 1.27 0.4225 0.8995 316 1148 11830 14024 -1.1335 8124.5 3705.5 9700 4324 0.4335 8547.86620530565 1.0516289947754 12.4208801357755 0.478261961081853 0.364140136386467 0.857031331226078 0.837542064852246
RP11-568A9 12430304 225 35788 28966.5 14572 481 9796 14553 79.5 74 24 28773.5 23612 14555 895.5 10263 14416 77.5 74 22.5 0.6875 0.6995 0.7065 0.63 1.3465 0.7515 0.958 392 1459 63185 51202 -0.5835 35307 27878 28485.5 22716.5 0.439 63503.4168564918 1.56586478166302 14.4703462629789 0.504351625155497 0.5317596598423 0.892147855173022 0.862684306009605
RP11-272A1 12430304 245 7770.5 9602.5 5842.5 354 469 553.5 100 100 0 3539 4381 2548.5 915 943.5 291.5 100 99 0 0.3615 0.38 0.367 0.362 1.3475 0.392 0.918 460 1354.5 10040.5 12714.5 -1.473 7416.5 2624 9248.5 3466 0.3905 6719.59026888604 0.925881972495183 12.074984463592 0.416239015030417 0.378309173785064 0.752189919149618 0.790384742337161
RP11-542O22 12430304 240 14372 17057.5 9574.5 399.5 1041.5 3597.5 97.5 75.5 0 7655.5 8745.5 4591 987.5 1152 1143.5 99 91.5 0 0.478 0.4655 0.464 0.463 1.271 0.441 0.8975 460 651.5 20640.5 24416 -1.065 13972.5 6668 16658 7758 0.3905 17075.5441741358 1.2233707457881 13.2324218835786 0.471581704429932 0.436464531970052 0.858573608234547 0.837388922601593

Total number of rows: 2925

Table truncated, full table size 985 Kbytes.




Supplementary file Size Download File type/resource
GSM185174.gpr.gz 760.0 Kb (ftp)(http) GPR

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