NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM185465 Query DataSets for GSM185465
Status Public on May 08, 2007
Title Unknown primary site, Melanoma, NOS (13111052)
Sample type genomic
 
Channel 1
Source name TB3073DF1T10
Organism Homo sapiens
Characteristics Tissue
TB3073DF1T10
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 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 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 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 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 13111052 150 27017 26723 5168 1127.5 1231 694.5 100 100 0 19566.5 19287 4075 1071.5 1158.5 766 100 99.5 0 0.714 0.7115 0.7125 0.7025 1.1865 0.7205 0.9715 156 573.5 44384.5 43811 -0.4865 25889.5 18495 25595.5 18215.5 0.8565 21593.6952714536 0.833326602217451 14.4152065646002 0.788988060820023 0.806749929283983 0.985410489144184 0.98858068596352
RP11-69E9 13111052 145 28101.5 30116 9910 1062 1316 1308 100 100 0 26420.5 29641.5 11491.5 927 1114 1171 100 100 0.5 0.9425 0.9885 0.9635 0.9715 1.1345 1.037 0.975 156 701.5 52533 57768.5 -0.087 27039.5 25493.5 29054 28714.5 0.8325 30622.8228228228 1.13185639545322 14.6792378175516 0.612332001884159 0.670960097131972 0.887954036983188 0.930760762364576
RP11-67E18 13111052 125 2617 2638 801 1051 1222.5 1393 56 37.5 0 2261 2264 644.5 926 1031 956 63.5 44.5 0 0.8545 0.844 0.8475 0.84 2.148 0.6905 0.536 118 569 2901 2925 -0.2275 1566 1335 1587 1338 0.836 1596.88995215311 1.0221693159625 10.4894035113141 0.715150834082509 0.695760260721211 0.952850877192982 0.950304164554413
RP11-291C17 13111052 150 11897 12563.5 4697 1024 1117 616 100 100 0 9179.5 9646 4043 905.5 973.5 488 100 100 0 0.7605 0.7585 0.741 0.7435 1.2555 0.798 0.9345 156 853.5 19147 20280 -0.395 10873 8274 11539.5 8740.5 0.8305 9962.6730885009 0.915704228722461 13.20845179198 0.579801507973539 0.624764563531494 0.945911174841909 0.943607994798102
RP11-506N24 13111052 145 14831.5 14558 3580.5 1039.5 1170 1019.5 100 99 0 11418 11202 2959.5 932.5 1052.5 1009 99.5 97 0 0.76 0.7595 0.7585 0.7485 1.2275 0.7725 0.9565 156 675 24277.5 23788 -0.3965 13792 10485.5 13518.5 10269.5 0.841 12467.8953626635 0.903649008541988 13.5530288449952 0.735031793797115 0.753405285366528 0.979589125844308 0.980204862554392
RP11-262N9 13111052 145 17534 16954 6091.5 1247 1393 889.5 100 99.5 0 19458.5 18451.5 7055.5 1073 1167.5 697 100 100 0 1.135 1.109 1.12 1.098 1.371 1.121 0.9355 156 667.5 34672.5 33085.5 0.1815 16287 18385.5 15707 17378.5 0.836 21992.2248803828 1.35779020192887 14.0692765792025 0.607223035942477 0.627702043299081 0.944161400664243 0.96561993416555
RP11-498J1 13111052 140 14179 14418 4533 1084 1419 2017.5 99 94 0 14028 14160.5 4670.5 1031.5 1303 1780.5 99 96 0 0.994 0.985 0.9805 0.981 1.1955 0.9935 0.966 156 681 26091.5 26463 -0.009 13095 12996.5 13334 13129 0.834 15583.3333333334 1.19169828758418 13.6694897079813 0.670375575769529 0.686300341419667 0.974523179425183 0.96582166764255
RP11-335F1 13111052 150 9128 9924.5 4362 1151.5 1501.5 1798.5 99 94.5 0 5726.5 6461 3649.5 976.5 1257.5 1375 97 81 0 0.596 0.626 0.6025 0.599 1.359 0.705 0.8945 156 654.5 12726.5 14257.5 -0.7465 7976.5 4750 8773 5484.5 0.836 5681.81818181818 0.712920469726225 12.5837992703003 0.42417276889128 0.551533220754819 0.866363805149812 0.910308796107198
RP11-260B11 13111052 150 10542.5 10298.5 4246.5 1089.5 1797.5 3387.5 84.5 64.5 0 9093 8905 4094 1007 1631.5 3242.5 81 59.5 0 0.8585 0.8565 0.8425 0.8355 1.297 0.918 0.95 156 634 17539 17107 -0.2215 9453 8086 9209 7898 0.8425 9597.62611275964 1.01876414906994 13.0912152667711 0.542073566186672 0.588164840473808 0.949845019528687 0.974654275917719
RP11-367E10 13111052 170 9920 10874 4442 1107.5 1229.5 770 100 99.5 0 8057 9079.5 4192.5 1011 1106 675.5 99.5 98.5 0 0.799 0.826 0.8035 0.797 1.2875 0.874 0.927 208 520.5 15858.5 17835 -0.324 8812.5 7046 9766.5 8068.5 0.836 8428.22966507178 0.955486654864862 12.9407913770482 0.537461207256898 0.591610213252036 0.872135405411097 0.901760561161244
CTD-2341I10 13111052 145 17707 18332.5 5710.5 1111 1334 1848 100 100 0 15089.5 16255 5793 1010 1164.5 1632 100 100 0 0.8485 0.8855 0.8745 0.8735 1.1835 0.9155 0.9585 156 677 30675.5 32466.5 -0.2375 16596 14079.5 17221.5 15245 0.8325 16912.3123123123 1.01892334146151 13.8962486879937 0.6436056700161 0.688815536479896 0.922353924022727 0.962823348822019
RP11-490K2 13111052 150 14699.5 15123.5 6887.5 1133.5 1302.5 1043 100 100 0 10843 11064 5242.5 1011 1145.5 868 100 98 0 0.725 0.7185 0.7145 0.7045 1.2235 0.746 0.963 156 659.5 23398 24043 -0.4645 13566 9832 13990 10053 0.853 11526.3774912075 0.849670181331039 13.4910697033961 0.526698677637312 0.54540248365965 0.913487478245621 0.909212436958205
RP11-491P10 13111052 140 19710 19161 6043 1078 1618 3285 99.5 91.5 0 14987 14700.5 5229 954 1408.5 2951.5 96.5 87 0 0.7535 0.76 0.7645 0.7435 1.2545 0.7775 0.9575 156 639.5 32665 31829.5 -0.4085 18632 14033 18083 13746.5 0.836 16785.8851674641 0.901692056987953 13.9807384490651 0.645407351588333 0.685162389594849 0.960396171128551 0.970513857229385
RP11-43H17 13111052 145 13794 14791.5 4719.5 1023 1311 1549 100 100 0 10468 11034 3811 955.5 1162.5 1445.5 100 97 0 0.7435 0.7315 0.726 0.724 1.1805 0.7765 0.948 156 661 22283.5 23847 -0.428 12771 9512.5 13768.5 10078.5 0.8325 11426.4264264264 0.892934832996765 13.4217649404744 0.651785120502388 0.678860929352662 0.941427037088914 0.926363073709456
RP11-492D3 13111052 170 11942.5 12680 6845.5 1031.5 1226 1852 92.5 85 0 7493.5 8193 4823.5 900 1025 1377 88 82 0 0.6045 0.6265 0.622 0.587 1.5395 0.6515 0.9145 232 499.5 17504.5 18941.5 -0.7265 10911 6593.5 11648.5 7293 0.836 7886.96172248803 0.722907870979566 13.0496315814365 0.408927986751039 0.458622594409895 0.904558098184553 0.937266616671486
RP11-97J12 13111052 155 14844.5 15903.5 5687 1040 1546 3184.5 99.5 97 0 9712 10908.5 4571.5 957.5 1345 2628 99 87 0 0.634 0.6695 0.6585 0.6565 1.2735 0.6825 0.913 182 617.5 22559 24814.5 -0.658 13804.5 8754.5 14863.5 9951 0.836 10471.8899521531 0.758016160035435 13.4226946417992 0.583264399042925 0.64587902134071 0.881637294206024 0.932128986979696
RP11-541N19 13111052 155 15134 15314.5 5726.5 1126 1790 3060 98 79.5 0 9980.5 10554 4436 968.5 1482 2460.5 93 68 0 0.643 0.6755 0.6665 0.655 1.4965 0.686 0.923 182 563.5 23020 23774 -0.6365 14008 9012 14188.5 9585.5 0.836 10779.9043062201 0.769390585135538 13.4437946311563 0.57697610278149 0.622285154813569 0.936617219529248 0.956262632838702
RP11-25L9 13111052 160 18410 19711.5 9070 1024.5 1262 1616.5 99 94 0 16997 18657 9192 925.5 1122.5 1432 97.5 93 0 0.923 0.947 0.929 0.914 1.3305 0.9755 0.9595 208 609 33457 36418.5 -0.1165 17385.5 16071.5 18687 17731.5 0.836 19224.2822966507 1.10397159507326 14.0252539700811 0.497623520754034 0.534486141685395 0.907151606955285 0.930874244885636
RP11-347O8 13111052 155 14598 14848.5 5811.5 1075 1341 1573.5 99 95.5 0 12505.5 12873 5557.5 960.5 1199.5 1633.5 96 89 0 0.855 0.866 0.853 0.8375 1.2605 0.8925 0.9635 182 629.5 25068 25686 -0.226 13523 11545 13773.5 11912.5 0.8425 13703.2640949555 1.01479918088471 13.5930635762167 0.553885921682532 0.59659534366326 0.938619132598757 0.940760312327306
RP11-518H12 13111052 160 14494.5 15439 6221 1100 1398 1624 99.5 95.5 0 10161.5 10718 4704.5 1016 1299.5 1560.5 96.5 87.5 0 0.683 0.677 0.668 0.6575 1.311 0.701 0.9305 208 654.5 22540 24041 -0.5505 13394.5 9145.5 14339 9702 0.8565 10677.7583187391 0.797260543056896 13.4315366430208 0.55830675537492 0.593951101916072 0.943236431226615 0.934834562270941

Total number of rows: 3857

Table truncated, full table size 1318 Kbytes.




Supplementary file Size Download File type/resource
GSM185465.gpr.gz 874.0 Kb (ftp)(http) GPR

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap